I do like a meta game idea. The concept of dropping 20-40 hrs into a map and then just starting over eventually causes me to stop. I'm a glutton, so it does take a few hundred (couple thousand from WoM on) hours.
Back in the old day with marriage/dynasties - would have been cool to keep track of a dynasty/family name/progress.
Now could be tied to a specific race - when you 'start' or 'reset' the game you keep track by race and/or sovereign in terms of score, time, kills/spells/quests/etc. Whether the SK was defeated, etc. IMO, that should be basic.
Maybe then tie it into rewards for replay - better starting gear (up to you if you use it), improved starting city stats, improved stats, etc, etc. So you could play the game normal/standard at will but there was also a reward for playing it many times.
Ideally, don't tie it to winning. Possibly some other mechanic, (related to map size, time, shards, players, etc) since many times the game will slog and I'll restart because I like early/mid rather than late game. Haven't played SK a ton yet, so might be different.
Random roguelike - dungeonmans - has a nice mechanic. The ability to start stronger on each successive playthrough - so yes, you need to go through the early game every time but its incrementally easier each time. Or not, up to you whether you use the benefits. Not a new idea, but done in a relatively sleek fashion.
Major gripes about the 4x system:
Each game is significant in terms of time/fun/thought - but once the map is over its gone. In some games there is a scoreboard at least, but its very minimal. Some of these huge maps takes 10's of hours (can be longer) and there should seemingly be some residual affect. I haven't played it in forever, but seem to recall dominions had a nice recap ability or something.
The end game can become a slog. Unit micro, city micro, gathering your forces, etc, etc. Especially at the higher difficulties. Streamlined methods are nice:
That FE spell that pulled all your armies to one area. The ability to cripple/kill a civ by killing their sov. Spell of winning, etc. It was the quest victory for a long time, you'd find it and when you got bored you'd kill off the big guy and win. Get your temporary score screen and then move on to the next map.