SotS2 still isn't great. It improves with each update, but I wouldn't pick it up yet.
As for SotS v Endless Space, I'll side with SotS.
Endless Space is highly derivative. This isn't necessarily bad. In fact, what it borrows from the MoO series--heroes, planetary features that drive specialization--are done well and serve as some of the game's better areas. What it borrows from GalCiv--the shallow, extremely dull, rock-paper-scissors combat--is an utter waste of time. (For those of you who haven't played it yet, you have no control over your ships during combat.) They tried to spice it up with action cards and the three round engagement system, but there's only so far you can polish a turd. Playing ES, I get the impression that combat was a complete afterthought.
GalCiv's shallow combat and lack of tactical depth was excusable because the rest of the game's mechanics fostered a much deeper strategic game. I think it would have been a better game with a more robust combat mechanics, but the lack thereof did not limit the experience.
SotS (and the theoretically "completed" SotS2) is in many ways GalCiv's bizarro-world twin. It lacks a fair bit of the strategic depth that GalCiv is built on, but it features what is likely the single greatest combat engine of the genre. There is a level of tactical depth (and player control) to combat that no other 4X has can claim. And, as is the case with GalCiv, the tactical depth make the more shallow strategic game excusable.
For my money, the last game to come out to successfully combine both tactical and strategic areas that were both deep and rewarding was Space Empires IV, released in 2000. 12 years has done very little to tarnish it. Any 4X lover should pick it up for 10$ on Steam. Just avoid SE5. Avoid it like the plague.