First off, sorry to post twice in one night...more ideas came to me. Secondly, some of these ideas have been expressed before, so I'll try to keep it short as possible.
1) Enhanced diplomacy/espionage:
- bribe barbarian villages to attack rivals or stop attacking you
- assasinate enemy great, scientific, or religious leaders
- bribe rival leaders to defect: high culture, and some gold would
be required: scientific leaders would be more likely to defect to
scientific civs, religious leaders to religious civs etc. I think the
aspect of individual men being able to lead a civ to glory or ruin
with their wheelings and dealings is something missing from
the game.
- Mutual non-agression pacts
- demilitarization: as part of peace negotiations, demand your
enemy surrender some of his military over
- Resource stealing: Steal resources that are renewable, like
horses of silks. Obviously, you can't "steal" iron or something
that must be dug out of the ground.
- Horses can appear once a civ has contacted another civ with
horses
2) Bring back the fundamentalist government
3) Revolutions can occur in unhappy, corrupt, and far-away cities.
1/3 of the units in that city defect, 1/3 are destroyed, and 1/3
escape to nearest city. The rebels form a new civilization of
whatever culture group the city was (possibly as one of the
civs not playing) This fledling civ starts off with double culture,
the same techs as the civ they broke from, and in a golden
age to actually give it a chance.
4) Rights and civil liberties: certain advances will trigger
unhappiness over civil liberties. Rights may include:
- Abolishment: no more slavery, makes the growing number of
abolishonists happy (triggered by industrialization?)
- Land ownership: creates happiness and avoides social strife,
but takes 1 food, 1 shield, and 1 commerce from city square
Certain governments require certain liberties. for example,
democracy automatically abolishes slavery, as communism
automatically forbids land ownership. All these changes would
allow for even further customization of your civ, and tyrants
would have very unruly populations
5) Natural wonders: special tiles, like "Mt. Fuji" or "Victoria Falls"
that give moderate bonuses.
6) Pollution patrol: Workers remain in fortified posistion until
pollution pops up, then they automatically go to clean it up.
After pollution is cleaned, they return to fortified posistion
7) Artificial synthesis of rubber, silks, dyes in modern era. Perhaps
a "synthesis plant" improvement that gives those resources to
a city where it's built.
8) Resistors or unhappy citizens may turn into guerilla units (more
modern barbarians?) that harass you.
9) Immigration: High culture, more civil liberties, and a more
representative government causes rival's citizen's to join your
neighboring cities one citizen at a time. "immigrants" are not
immediately productive citizens, however an "immigration
office" improvement will assimilate them more quickly (wonder:
Statue of Liberty; immigration office in every city)
10) Modern infantry, early atomic unit, attack choppers, and units
with both attack/defense and bombard (such as
crossbowmen, bombardiers etc.).
Overall, I think many of these would improve the game. As it stands, the most powerful are those gifted with the strongest traits or best land. Some of these changes might make the game more dependent on cunning, social manipulation, and shrewd diplomacy. Sorry for the length of this post, by the way.
might actually be able to offer useful enhancements. Anything from better 'bot players to a spreadsheet-like diplomacy screen.
)
I haven't thought about sea/air... 
