Just going through the Civ 4 Fall from Heaven Mod and tallking with my friend re: Moo and Mom. I think one of the mechanics that made these games so enjoyable is what FFH(Fall from Heaven) called the "doublewin" mechanic. These are, in FFH, units that can only be built by players who have de facto already won, either through resources or size. The units are VERY powerful. This increasing Player enjoyment by being able to produce units that just run rampant AND has the effect of adding both tension and a sense of fear/inevitability to the end-game for players who have "already" won. Even in multiplayer these units would serve as a backstop against end-game sluggishness.
In both Moo and Mom, off the top of my head, I can think of units and/or upgrades that sped along the inevitable AND made you feel awesomely awesome:
MoM: advanced units, magic, and heros
MoM Paladins: anyone who is anyone did a Human paly rush at some point. So overpowered they are almost unfair. But yet you need a completely developed city with almost all upgrades to even begin to build a single Pally unit.
MoM Heros: Warax comes to mind thinking of uber stat-ed out heros that just could not be beat. To get either Warax, via summoning, or a good hero required lots of spell research or lots of leveing, respectively, which required LOTS and LOTS of time/battles. But after spending the time, you were rewarded with the unstopable.
Moo/Moo2 Orion/Antares Tech: Same mechianic really. You found Orion and beat The Guardian. You could only do this with enough tech to beat The Guardian. You gained some insane weapons, such as: death ray, black hole generator, etc. You could then build ships with these massive improvements and dominate.
I think we need something like this in singleplayer. It will give the Player something to achieve and add the knowledge that they really were able to dominate in the end. In multiplayer, some clever balancing could help to end end-game stagnation.
How to do this, I really don't know. But the "doublewin mechanic" is something I greatly enjoyed int he Moo's and Mom's of yore.