In my subjective opinion, Stellaris' biggest issue is the lack of resource scarcity. The infinite abundance of resources means that there isn't much to fight over for most of the game, it means individual colonies will matter less and less as the game goes on and it often leads to games stagnating until a crisis shows up.

Wars are fought over resources, over material gains, and in Stellaris it rarely feels like that. I rarely feel compelled to go to war with another empire because between megastructures, ecumenopoli, habitats and ring worlds, i can generate infinite resources regardless of how many planets and systems I control. This wouldn't be as much of an issue if Stellaris had victory conditions outside of military victory, if you could win through diplomacy, science, faith or whatever like in Civilization, but with how the crises are designed, it's very apparent that you're supposed to win through combat. But wars don't feel "organically incentivized" to me a lot of the time, if that makes sense. I don't feel like I have much to gain from going to war, I just do it because that's the only way to make the game end.

I think the game would be more exciting, dynamic and strategic if colonies and system resource deposits had a limited amount of minerals, food and energy you could extract from them before their output greatly decreases.

That way, there would be a much bigger incentive to fight over colonies, especially in the lategame. Because when you have 20 colonies in the lategame, one more or less doesn't matter all that much, but when only 3 of these colonies are still running at full capacity, suddenly that one untapped planet becomes much, much more valuable. It would cause conflict much more organically, as eventually the exploitable galaxy gets smaller and smaller until there is only one last empire standing. While the crises are cool (and I don't think they should be removed), I think they are a very clunky way to force conflict, and it would be much nicer if the endgame was instead determined by the friends and enemies we made along the way rather than an outside entity randomly entering the playing field so you have to actually fight someone.

This is, again, subjective, as I'm sure a lot of people specifically enjoy Stellaris for its chill, relaxing pace that allows you to watch youtube on your second monitor while effectively playing stardew valley in space. I enjoy that aspect of it too sometimes, but still, it eventually always falls short for me. Wonder what you folks think about this.

Edit: I realize that this would be way too fundamental of a change to ever realistically make for the devs or a modder, as you would have to basically re-design and re-balance everything from scratch. This is purely theoretical.