I feel the way they are done in IR is cool. Yes they are still railroady giving you claims but its not a big deal because of the way the game plays. In fact there are many times where i completely forget about them and the game plays the same. The bonuses are very small so its nothing game changing.
Also one mission tree blocks the other so if you pick the development tree you can keep expanding doing your thing but you will do It without the missions claims, which as I said, it doesnt make a huge different so thats why i forget to use the missions so many times. Jut they do make for good flavour without being overpowered.
The military rewards are almost non existent, and there are very few rewards that are massive economic modifiers. They usually involve higherr rate of pops conversion, giving you pops, giving you building capacity in a city and things like that. These are things that feel nice to gain but that dont really overpower you, you still have to work to improve, you still need to build your cities, build your trade, your production, etc.
Also, you are thinking with the EU4 mindset which is a mana fest. In IR Rome when you get claims for a mission and you complete the mission, the newly conquered land is usually worthless. Lots of angry pops, rebelions, very little to no income. You need to invest a lot of work and money in the newly conquered territory until it starts paying off. Most of your increased revenue will come from improving your economy in your homeland.
So "winning" a province through missions feels good bc your country looks bigger on the map but its not like in EU4 where you core it all and in a year its giving you full profits. I am quite convinced that thanks to the pop system EU5 will work similarly and new provinces will take a long time to assimilate, rebuild etc until they start giving money. Also I a sure that the rewards will be more akin to IR, as I mentioned, and they will give small bonuses like movemebt of pops or pop attractions or building capacity or higher conversion rate and things like that, but nothing like in EU4 with massive bonuses etc to railroad your country. The good thing about no more mana and having pops is that the game system allows for simulating real situations that lead to real outcomes, so they dont need to force them like in EU5 with ridiculous bonuses and things like that that "shape" your nation. I am sure the bonuses will be small rewards that simply slightly help you should you decide to pursue X course of actions but you will still need to put the work and time.