4X games are complex. They are, effectively, simulations of reality; however, they are also games, and in order to succeed in that role, certain rules must be observed. This, I think, is why Manifest Destiny died.
Rule #1 - Games are abstractions.
It is impossible to completely model reality without a quantum computer, and a quantum computer with the ability to perfectly replicate Earth would be exactly the size of Earth.
Games simplify reality in order to present a carefully constructed entertainment experience for players. While it may be an interesting mathematical exploration to model the shifting of tectonic plates programmatically, it does nothing for the game itself. "Realism" in a game is not the modeling of reality but the appearance of it. Sid Meier himself follows this rule.
Rule #2 - Games are themed.
By this, I don't mean "sci fi" or "4X." I mean that any game should be able to be summed up in one sentence. As an example, here are a few one-liners that you may recognize:
1) Destroy anything that moves to repel an infernal invasion on Mars.
2) Design a creature and take it from the cellular stage to the galaxy-spanning empire stage, evolving it as you go.
3) With your friends beside you, gradually develop a character in a highly stylized fantasy world and battle the forces of monsters, demons, the undead, and an opposing enemy faction.
This single sentence should drive the design of the game.
Rule #3 - When in doubt, cut the feature.
If a feature's fun factor or playability comes into question, shelve it for a later version or cut it altogether. The core theme must remain intact at all costs.
After exploring all that, here's my take on Manifest Destiny.
The core theme of Manifest Destiny, the single sentence, might be this:
Design your own race and take them from cave-dwellers to futuristic empires as you battle with other players for world domination.
This seems to capture the essence of what you were trying to accomplish. To support that, here are the four key focii:
1) Race creation and development
2) Technological research
4) Strategic warfare
If a feature doesn't directly add to one of the four focii without overburdening the others, it should be dropped from consideration.
Manifest Destiny had potential, but not in its current state. Much needs to be trimmed before it can be refined into a wonderful game.