hmm lets see what i can come up with from the top of my head.
-vastly improved ship designer
-hexes
-combat expanded, things like range accuracy speed etc now factor in.
-multiplayer
-steam workshop (not 100% confirmed but makes alot of sense)
-it looks alot prettier
-political party system overhauled, not sure to what yet
-carrier ships added
-fleet mechanics added, i.e. escort ships at least. possibly formations etc.
-adjacency bonus minigame on planets added
-heard some rumors about a colony adjacency system coming too.
-rumor that espionage won't be in the initial release but not 100% on this
-tech tree now has specialization research and "tech ages"
-strategic resources added. not sure what is happening with galactic resources from galciv2.
-more terrain features added, like nebula and dust clouds. presumably more, the anouncement screenshot/art had a blackhole and a binary star.
-starports are now space based rather then planet based.
-ideology system added
oh and the drengin ate all the torians.