My biggest problem with SSE2 is with how boring late-game is. There's no incentive to build colonies unless the server is dying. I would add some sort of statistic in the main menu showing how many bodies you've made a colony on, and what bodies you've never made a colony on.
Another idea I have is that there could be an extended plot in late-game, but I think SSE2 is a bit too far into development to make an abrupt change like that.
But that's just my opinion, what problems do you have with SSE2? I just wanna start a bit of conversation and see what people's opinions are.