Johan, I think there are several elements to the negative community response. First, there's been built up tension recently with the DLC model, particularly revolving around EU4 Immersion Packs (and the swarm of bugs in Megacorp); with a new game being released that appears to lack flavor and suffers from some (understandable, yet major) issues, the first instinct for quite a few long-time fans is to think "well, they're just going to fix it with DLCs now", and that can inspire a great deal of frustration.
The second, is that there was some press about this being the most polished release yet; while true (remembering Vicky 2's Jacobin swarms of death on release and other gamebreaking bugs) and certainly is a step in the right direction for future releases, it doesn't mean was free of some glaring launch issues (e.g., incomplete localizations and performance issues) that people expect better of, feeding back into point 1 (and the marketing/hype surrounding I:R). Benefit of hindsight and all but more time for the development cycle would have helped address this, though obviously you are under financial, time, and manpower constraints for any game design/development project.
While this is suppose to be a sequel to EU:R, few if any of your current fanbase will have played that game, and the standard of comparison would be EU4 and CK2. Yes, it's really unfair from a developer standpoint; those games have had years of post-launch releases that have made them into amazing, immersive experiences. However, from a consumer standpoint, those are now the gold standard of the genre and what new releases are held to; it's unreasonable to expect customers to compare a game to one published over a decade ago vs, a game they probably played yesterday, or even to the release states of aforementioned games. E.g., CA's new Three Kingdoms Total War will inevitably be compared to their Warhammer II game, even though it's a new series with an entirely different setting and focus; if they released a Rome III, it would be compared to their other current titles (or similar games, theme or play-style, on the market) as opposed to Rome II, despite being the direct sequel.
While I'm certain there are people who are just complaining for the sake of complaining, usually those voices would be a very small minority; however, quite a few of your fanbase, including long-time loyal fans, are not happy with the release. I think it's essential to understand the roots of the frustration and acknowledge that it is at least valid, from a customer standpoint (if unreasonable for the development side of the equation). Certainly, my experience playing with Imperator has been that some aspects of the game are unfun or downright hostile from a UX perspective, particularly with how un-intuitive and, to put it bluntly, bad, some of the UI is, particularly around navigating characters and families.
I'm going to try and be as thoughtful as I can in responding with constructive criticism of I:R, as I genuinely do want to see I:R flourish as a game. I'll break it down into 3 levels of criticism; macro/design criticism, implementation, and "details" (bugs, UI, etc.). Spending some time reflecting, I think most of the issues people are having with the game fall under the "implementation" category, being larger than mere "bugs" and fixes and require major updates, but not requiring a complete overhaul in the same way Stellaris required the pop-system to be utterly replaced, root and stem, in Megacorp, or the condensing of the 3 FTL systems into 1 organic (hyperlane-based) one.
I would also note some of the positives of the game: the map is absolutely f**king gorgeous and fun to play with; the terrain design all works well and provides interesting strategic options. The combat system itself is quite innovative and far more engaging than most Paradox games (though necessarily needs tweaking for balance).
Game Design
I think you had a very ambitious plan going forward with I:R; it borrows a great deal of features and aspects from many other Paradox titles, and has at least successfully implemented many of them in a way that can be built off of. E.g., while I have some issues with it and, IMO, believe (potentially major) changes that need to be made to it, the pop system is workable and doesn't need to be removed entirely or replaced with another abstraction. Most changes and requests build off the systems you've put together.
The main game design decision that people are taking issue with is the 4 Powers/"mana". I don't necessarily take the view that "mana" is bad per se. Some level of abstraction is necessary, and the introduction of Monarch Points in EU4 was a interesting and necessary change from EU3 to provide better strategic play/thinking. Moreover, at this point it's central to the game design, and planning around it is necessary. Do I like it personally? I'm ambivalent, however I do think it's been poorly implemented, and some of the many choices that have been assigned oratory power usage or other power usage should not be. I'll discuss it in my next section.
Implementation
This is where I think there is a great amount of room for growth, and where most of the criticism can be addressed. The game just doesn't feel interesting or unique in the same way that the other Paradox titles do, given how much it is inspired and borrows from all of them, yet doesn't do anything revolutionary with them. Some of my personal suggestions and recommendations for target updates:
1) The building system seems muddled and there isn't much planning involved with them right now. Break down the bonuses further, and make their effects more powerful/noticeable; granaries could just be pop growth (with a more powerful effect), and a new building can be focused solely on slave happiness. Giving lots of small bonuses, like the marketplace (5% income and 1 civilization level? eh) leaves people underwhelmed, because while we do know we've improved it, we don't really see the benefit and spamming lots of buildings everywhere doesn't really feel rewarding, it just feels like a clickfest. Have 1 building improve tax income, 1 building improve commerce, and 1 building that ups civilization level and civilization level gain. Perhaps a building that increases supply in the province (and neighboring provinces?) or research points. Either way, the goal is to provide players with meaningful choices in terms of building options, encourage domestic specialization, and make the effects noticeable and more pronounced; you could increase the cost to compensate for the increase in buildings' effective power, but make it satisfying to use.
2) Inherent imbalance and confusing implementation of the "mana" system. The inventions system and civic power is quite ingenious and a great example of it being used properly: you have to make strategic decisions about which inventions to pick up and whether to balance that with trade routes (though that part needs some bug-fixing). Military power is ok, but you mostly just spend your time saving it up for military traditions (which isn't really "engaging" to use). Yes, you use it for roads and mercenaries, as well as some other small purposes, but there's always a glut of military power so you don't feel constrained in any actions other than with traditions. Religious power feels useless; you use it for omens, stability, and converting pops, when there is a governor policy that lets you convert pops automatically; I suppose stability can be burned for no-CB wars, but that's more an MP consideration. On the other hand, oratory is very much over-used.
Why does declaring war cost no oratory, but insulting and improving relation do? Why does changing governor policy require oratory and cost a negligible amount of tyranny, when in fact you could just have a hefty tyranny cost attached (representing the tyranny of forcing local governors to adopt central policies)? Heck, why does bribing characters (and other character interactions) cost oratory/various powers? Too much reliance on oratory power as a mechanic, and that's why people have been bashing "mana". Swap some of the actions to rely on your other mechanics like tyranny or AE so those become more meaningful, and balance your 4 powers so they're all able to present meaningful options and gameplay (that doesn't feel forced and gated).
3) On the subject of governors, if you change those policies and your governor dies, you just spent points on something wasted and it just feels bad. Having manually chosen policies locked in for a set amount of years before local governors change to their personal preferences would be helpful. Also, if possible, fix it so higher civic governors are "smarter" in their choices (right now it just feels like a random crapshoot), so they don't try to culturally convert provinces that are 95% primary culture or something, or pick borderlands policy in a province with low freedmen count/with no forts. Lower civic governors can be more random, to represent incompetence. Some transparency in how they select their policies could help too, and then lock governors in for a set time like generals.
4) Characters and families aren't fleshed out; beyond the lack of real genuine control or influence over them, the ability to interact with them is also rather limited. This isn't CK2 and it shouldn't be, but as it is I really just don't care at all about the characters, who they marry and if they have children, and am not invested in the domestic politics of the nation at all. This could be a rich vibrant world and an area for immersion during peacetime, and I don't feel it at present.
This also feeds back to criticism of "mana", because there feels like you have limited control over the amount you get. You can spend your time boosting someone up in popularity and prestige with triumphs and such (another aspect that could do with some flavor; granting a triumph or hosting games feels bland and uninteresting, and instead of a random tooltip, an event chain ala. CK2 would make it more interesting and engaging; IIRC, those were in for Great Hunts/Feasts/Markets on launch). How party leaders are chosen for republics feels like a black box: all the old men with terrible stats seem to get that position. Random marriages are also broken, and thus leads to the death of families as all the young heirs fall prey to those dastardly cougars.
Expand on the character interactions, and providing more options on that front (as well as removing the need to spend state power points on it [the part I question most]) would provide players with the incentive to actually care about the people in it, as opposed to only when they start throwing a hissy-fit and threaten to revolt.
5) Religion & cultures need expansion, as only having military traditions being different between them feels...boring. While I understand the decision to make religion (and to an extent culture) similar across all of them, it really detracts from your game, as both of those played a major role in the game's time period. Different religions and cultures should play differently mechanically, not just solved with flavor; CK2 does it quite well, but even before Holy Fury, small things like cultural retinues and tactics, options to loot/raid, etc., were tied to culture which made it a relevant and engaging part of the game.
On that topic, wrong religion and wrong culture effects and penalties on your country need to be re-evaluated; the Roman Empire was a multicultural and multi-religious entity, and it should be viable to try and play like that. Instead, you are encouraged to immediately convert and assimilate all your conquests ASAP (province loyalty allowing), with an efficiency that would be impressive even in a modern state. Perhaps instead of impacting all pops equally, some pops (like citizens) would care more about religion and culture than others.
6) Diplomacy needs some focus on that topic. Right now, it feels confusing, simplistic, and restrictive, somehow. Actions are mostly gated by oratory power more than anything (which is not a good thing).
Ways to change it, for instance, include sending characters on diplomatic missions to improve relations (with their oratory determining how much they improve relations by), and locking it for a few years. Something like that would allow you to tie the systems together (the systems don't quite feel interconnected yet), provide avenues to improve character interaction and management, and also allow you to expand on the systems there; for instance, the diplomat might get bribed to defect to another country, etc. As oppose to locking the action behind oratory power to prevent spamming, make it play into other systems; for instance, AE being used to pay to fabricate claims (or send characters to fabricate CBs in foreign provinces). Overall, just rely less on using state resources for it.
7) Pop movement and conversion in general, particularly the buttons allowing for instant promotion/assimilation, need to be looked at; spending points and spamming clicks to convert pops just doesn't feel necessary. It's not a rewarding feature from a player perspective, and makes pop management feel boring, particularly when pops don't do things on their own (which is a core feature of Victoria 2 pops or Stellaris with immigration).
There are more, but I've spent far too much time on this and am tired.
Bugs/Fixes
Too tired from writing the other one, but I think everyone provides ample feedback on this and I trust you'll address them in time. Some ones I'd like to see changed:
1) Trade Route request spam is frustrating (I get nations that keep asking for the same resource from the same provinces several times still in 1.02). When my trade routes break, a reason would be nice for me to know why I wasted civic power on a failed route.
2) UI needs a ledger or something that lets me search my characters by name or trait (like CK2), or sort through my families. I'd like to be able to see other nations' families/characters too, because these days I'm mostly gambling when I'm choosing to execute or welcome families to my nations.
3) Fixing attrition in home terrain: e.g., always having attrition in your capital as Moslyon despite being below attrition cap by far.
One suggestion I would have for a future update:
Tie standing cohort size to manpower in some way; right now, you can just keep raising larger and larger armies so long as your economy can sustain it, which leads to very unrealistically large doomstack sizes late game. E.g., your max manpower is 100,000 and you have a standing army of 50,000 (50 cohorts), your manpower recovers -50% to reflect the amount of men you already have in service. This would make attrition more viable and provide smaller states with the ability to wear down larger powers, and is a more elegant way to control army size than EU4's force limit; it's something the game probably needs anyways. You could probably bump up the amount of manpower that you recover on a monthly tick to compensate, finding a break-even point somewhere.
EDIT: Note, I know all of these suggestions come from someone with no clue as to how the coding behind the engine works, and the possibility of any of these features or the amount of work hours that would go into any of it. I've dabbled in modding, but that means nothing.