MoO2:
Pros- The granddaddy of them all is still one of the best in the business, with compelling ship design, a good tech tree that naturally creates more diverse empires in game by forcing them to make choices instead of researching everything, and general all around good performance.
Cons- Where it falls short however is in its empire/species variety. If playing with all possible AIs there will always be one of every stock race, and there is no option for AI customization, you will always be playing against the same set of aliens no matter what you do. It also suffers some severe balance issues, specifically the Psilons, who fly in the face of the tech tree limits and get to have everything, making them far and away the most powerful race in the game pretty much by default.
GalCiv2:
Pros- This one introduced me to the genre, so I have fond memories of it, specifically the rather intricate diplomacy and racial diversity. It also features a tech tree that includes quite a few more "steps" then most other games do, making the late game come later and making it less likely that empires with crap research will catch up just because the science guys hit the limit. The techs for the races feel somewhat more diverse as well, instead of the typical "one unique tech per race" each tree is totally different, not just in unique techs, but in how fast certain shared techs are acquired.
Cons- Rock/Paper/Scissors combat, while the ship customization lets you create incredibly diverse ships aesthetically, they will all be nearly the same functionally. Additionally this makes many of the differences in the tech tree nearly meaningless. It has a balance issue in that all "defense" techs are insanely cheaper then their "attack" equivalents, and not only is the AI not aware of this, but attack and defense are calculated equally in combat, creating a fairly large exploit early on.
Stardrive:
Pros- Probably the best ship customization I've seen, somewhat similar to SR2s "painting" but it encourages you to actually think about where you're placing things internally, if your antimatter reactor is on the edge of the ship, you will have a dead ship very quickly. It lets you create chokepoints with bulkheads, armor, and shields (which cover a set area in the ship, meaning if your engines aren't in the circle, they have no shielding) and even allows control over the firing arcs of turrets and lets you create craft that can fire in all directions if needed.
This extends to stations/bases, but these can be built anywhere in space instead of just around planets, letting you equip them with warp inhibitors or such and create defensible areas away from your precious planets.
Cons- VERY shallow tech tree, and everything in it is practically a cookie cutter space tech trope. Supposedly its still in development, but that development is terribly slow. It also operates on a relatively small scale compared to other games, and has the same "AI only stock empires" problem from MoO2. The empire's tech trees also are all exactly the same, not even a unique racial tech in the game.
Distant Worlds:
Pros- Soooo many starting options for this game. You can pretty much custom tailor every aspect of the universe if you want. It also feels somewhat more "epic" in scale, starting you earlier then other games. You will actually feel proud when your first warp capable vessel launches instead of it just being that ship you start the game with. I also rather enjoy the way different stellar phenomena can have effects on stations built near them, so you can have REALLY scenic nebula or black holes that give you a research bonus. The same goes for planets on a lesser scale, and it makes everything feel more unique.
Oh, and I like its planetary invasion mechanics, they are slightly less bare-bones then others in the genre.
Cons- Pretty much just reread the cons section for Stardrive, minus the small scale and development things.
Endless Space:
Pros- Wonders. Just...Wonders. They feel really...wonderful... the tech tree is pretty nice too. Can also get pretty big in scale, though I personally have only played smaller maps in it so far.
Cons- While the combat has much more depth then GalCiv's it still follows a similar rock/paper/scissors thing, so I have to con it. Even if it is very pretty.
Also does the "AI stock empire" thing. And that's terrible.
Star Ruler 1:
Pros- All the things except diplomacy. SR had so much freaking potential, between the stupidly hilarious scale the combat could reach to the pure awesome of sticking thrusters on a planet and flying it around just because you can and then designing a ship that launches LARGER SHIPS the game just let you do pretty much everything you could ever want. Except talk to aliens in a non-killy way. Or win, in my case
Cons- Diplomacy was ungodly terrible. I cannot possibly express that enough. Sorry guys, but that's just what it was. Seems like you're working on that though.
There was also the whole "BFEL is entirely unable to grasp how to do the things without failing horribly and inexplicably" but that's more a personal problem I suppose