Game designers have thought long and hard about this problem over the entire history of the genre. There have been numerous attempts at putting in mechanisms to slow down a player with a large empire but they often just make the game more tedious. I think this is the wrong approach. Once you reach an overwhelming advantage the game should allow you to close it out easily.
I think of chess at a high level. If no player ever resigned, instead forcing their opponents to perform extremely long, drawn-out checkmate sequences in theoretical win positions, people would hate it. Just resign so we can move on to the next game!
It's an issue I have with all of these infinitely replayable games, and a fundamental part of human psychology, I think. Most people tend to start lots of personal side projects, but not many can truly commit to finishing something worthwhile.
... because like a snowball, once you start rolling downhill, you only ever get bigger, which makes you roll faster, which makes you get bigger, etc.