My ideas to promote later end :
Make conquest/domination more difficult :
- promote AI gang up against strong military players, which in fact, often happened in history. Could be backed with strong diplomatic penalties to keeping a large army.
- Make CPUs stronger via better, of course!! AI
- Helping out-teched civ to catch up via different mechanisms, discussed in others threads. Don't forget out-tech is factor #1 in having a strong army.
- penalties to large empire, discussed many times in others thread
- possibility of civil war splitting the country, increased possibility with large empire. Captured cities/nations would have a high propensity to split up.
- possibility of colony, which would allow conquered civ to exist and reclaim independance later
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- different nuke handling, see other thread
In history, no civs have been able to keep control of the world by military ways. They all lost it one way or another. Large empires are rather unstable. It would be realistic and more fun to set many drawbacks to military conquest, altough keep it possible.
Make other victory options more appeling, long enough to acheive to reach future techs :
Scientific victory : Could take form of a big tech ( the spaceship), that should be researched after ALL future tech are discovered
Diplomatic victory : U.N. leader for more than 1 time, let's say, 3 times in a row, or something like that. Should be allowed to all civs once U.N. is founded. Remove 25% condition to be eligible. Only victory not relied directly on indirectly to a large empire

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Commercial victory : as in SMAC
Culture victory : keep it that way