Civilization: add more civics and techs and special resources, more civs, more units... It doesn't bring anything to the game. It just makes the excel more annoying to deal with. I paid for Phoenix Point (from the creator of XCOM). Nice game but when they asked for feedback it was just about wishing either more units or more maps or more factions, which would you prefer? None! How about making the core mechanic more fluid so there's less "oh I didn't mean that"? Or the crashing and having to start over after many updates.
What would really make Factorio better? I don't know. Maybe a simplified interface? There's so many ctrl-click things and having to place and stock turrets in a hurry that it just makes me not want to start the game etc.
I would say, still, that SE was the missing expansion so I've already had the expansion and I'm not that tempted by the new updates (Except for elevated rails!)
The SE author also showed impeccable taste in game design, improving on the base game, their beacon change being a good example, running over pipes another one.