Some people call great works of art flawed masterpieces. This is not one of those. This game is more like a flawless failure. Ignoring the bugs (which aren't really that bad TBH) it is difficult to see where precisely this game has gone wrong, but still leaves a bad taste in one's mouth. The early game events and exploration are brilliant, until you've tried it several times and realised that there just aren't enough different events. In contrast, the randomly-generated species try to make sure that you've never seen it all, but with every alien race generated by the computer there's nothing to get attached to or care about. The customisation options are vast, but you can never create the exact species that you've dreamt up. The galaxy is old and full of wonders, but you're left with a small number of fairly pedestrian government types and ethics and an ecosystem of mostly very conventional star empires.
Then there are the tried-and-tested complaints about how much of a chore the mid-game is and about how much of a focus is put on warfare. Minerals and energy credits are all ultimately used to build and maintain fleets, with buildings and technology being solely used to make resource extraction more efficient or weapons more deadly. Trouble is, war is boring and unproductive. Yeah there are space explosions, which is a plus, but in terms of grand strategy (this is a grand strategy game) war in Stellaris consists of chasing enemy fleets around the map trying to catch them. The side with the bigger fleet with always win an outright battle and the interface makes Fabian strategies and raiding a nightmare. The completely out-of-place EU-style warscore system also gets in the way. Great galactic conquerors are forced to give up occupied planets for no reason at all. Outmatched defenders can't use clever tactics to avoid battle since the AI will still be winning warscore somehow with their home front being demolished. There are no insurgencies, no pirates, no unconventional weapons like bio-weaponry or computer viruses, no weapons of mass-destruction. Not even a token Death Star or asteroid drop. Just grand fleets chasing each other, having grand battles and winning grand victories that were foregone conclusions due to ship design. Yawn.
The part of the game that is truly not yawn-worthy is interacting with primitive species and colonisation. Primitive civilisations are a great feature and it's really fun to imagine the primitive hu-mans down on their little rock reading the paper and laughing at the silly stories about cattle mutilation and alien probing, whilst your observation posts pump out masses of great data. Invading alien planets by force might not be very involved, but it feels pretty fun. Infiltration is great, with lots of interesting events, and I really hope that gets taken further. And ruling over diverse species with diverse needs and ideologies is also pretty cool. The frog people might make great warriors, but they're xenophobic and hate you for your brutal conquest, whilst the bird-men are only glad to become slaves. The pathetic hu-mans are are still sitting there in their primitive housing estates and skyscrapers, but soon you're going to get the money together to re-build everything and elevate them into the space age. If only the rest of Stellaris had this level of fun and involvement. Unfortunately, Paradox seems to have come up with this idea that this is all 'micromanagement', fit to be relegated to the control of AI sectors. Sorry, you can't colonise that planet your way, it must go to an AI. No more fun to be had here, go and start another tedious war instead.
This isn't Civilization, there are no peaceful victory conditions and there's no evidence of the march of social change or technological advancement beyond shinier factories and bigger warships. four years in, space doesn't really feel any different to how it did ten years in, or how it will feel 80 years in. Strangely for a company that tries to represent the whole timeline of humanity, this is a problem Paradox games seem to have in general. All technological change in Paradox games is incremental, all development neatly categorised into buildings of levels I-V. Sudden jumps and breakthroughs where everything changes and old tactics become obsolete are rather rare. And Stellaris, a science-fiction game about societies being changed by advanced technology, is particularly badly hit by this. The early game is pretty good, it should be said, because the early game technologies actually unlock really crucial new features. Colonisation requires a tech. Different weapon types require techs. Robots require a tech, as does genetic engineering. It would be really good if the tech system was designed more around those hard jumps rather than incremental increases, but unfortunately the semi-randomised tech 'tree' makes that too difficult to balance and Paradox traditionally doesn't like doing that anyway.
Stellaris, in my opinion, will be pretty difficult to rescue without re-building it from the ground up. It's not a broken game. Broken things can be fixed. The diplomacy I'm sure can be fixed. Buggy end-game crises can be fixed. Colony related events can be patched in. New mechanics can be added. Maybe sector control could be refined. However, at its heart I'm not sure the greatest problem, the lack of identity, the lack of meaning to your decisions, will go away. Stellaris could have been truly brilliant, in my view, if instead of a randomly-generated galaxy the developers had constructed their own fictional sci-fi universe, with familiar races that would make an impression on players. EU has recognisable characters like the Big Blue Blob and Blobhemia, and everyone cares about what's going on. France is beating up Spain again, England has colonised Florida, maybe Italy is going to form soon, all of those are part of a familiar, persistent world that we can learn about and remember. CKII has it's Karlings and their border gore. Victoria II is tightly-scripted and people really enjoy it when things go off the rails in unexpected ways. But everything in Stellaris is random. There is nothing persistent. Every alien race you encounter will be gone in the next game, there will be some other dudes with a wild portrait and a randomly-generated gibberish name. Why care about them?
EDIT: Replaced 'pre-sentient' with 'primitive', since they're not the same thing in the game.