Late game has some weird borders and expansions, as well as dead civs that have no hope of returning. In a post nationalism world, it is strange to continue to see large sprawling empires. At end-game, however, stability isn't hard to attain.
With that said, I think a U.N. Decolonization Resolution is a good mechanic to get to our desired outcome for a more dynamic endgame.
The Decolonization Resolution pops up every now and again, and targets one dead civ and tries to resurrect it.
For example, the Decolonize Mexico (if the US expands south too far), Decolonize Vietnam (French), or Decolonize Poland (Russia, et al.) Resolutions would, once they pop up, allow for the world to vote on supporting the guerillas and revolutionaries.
The U.N. vote also has a weighted 'Liberation Score' (which could be displayed next to the [Dead] marker for dead civs. The Liberation Score is a value proportional to the size and strength of the colonized cities. If the occupied cities have high stability bonuses (courthouses, religious bonuses, etc.), the liberation value is reduced, and vice versa (overextended, underdeveloped, and angry cities have higher liberation score).
The possible outcomes are:
- Vote Success: This triggers gives a 'Rise of X Civilization' pop-up that is similar to regular spawns for civs that own core cities,
- Vote Failure: This rotates the next Decolonization Resolution to the next dead civ in line,
- Vote Defiance: This gives the normal penalties to all defiant civs, and gives an additional angry citizens in the core cities of the colonized civ, which increases the Liberation Score and makes the next decolonization resolution more likely to succeed.
Decolonization also affects independent-ruled cities, with a succeess respawning the civ in the core areas.
Alternatively, of course, a general 'Rise and Fall' mechanic that is independent of U.N. Resolutions could also get the job done, but having it be tied to the U.N. gives a twist on modern diplomacy that is quite appealing.
Edit: Oops. I realized there WAS a decolonization and 'free nation' option in the U.N.
I think the Liberation Score idea (and showing the value next to dead civs) is still viable however, but perhaps changed to be called Rise score. It can be a core mechanic as part of the general Rise and Fall cycle of the game. A civ collapses, keeps a Rise Score, which fluctuates over time. If it reaches a certain threshold, it triggers guerilla troops and random liberation events, and contributes as an additional weight in the U.N. votes.
For example, when the U.N. vote on whether or not to restore a collapsed and occupied France (24 Rise Score), the Yes vote automatically has 24 votes from the Rise Score.