The main issue I still have with Endless Space is Warp. There's no choke points, no intercepting or blocking units until they reach your planet. I also don't like the cutscene battles; if I could just play my cards and have a quick battle, I'd be happier (last I checked, autoresolve never leads to anywhere near as good an outcome as manually fighting). AI diplomacy is also a tad simplistic, and I tend to play 4X games singleplayer so that sucks.
Drifting back off topic: we should be able to do massive space battles these days. I'd love to see a new X-Wing/TIE Fighter game with a few hundred ships flying around at once. I'd expect that a competitive Space Sim would be cheaper to make than most other genres these days; you have ships, effects, and UI to create. No levels, no level design, no environment art, little to no character art, few if any animations...
Edit: choke points, not "checkpoints"
This comment was edited on Jun 26, 2012, 22:48.