My two cents... or maybe twenty-three cents...
V. Soma -
My idea: Military units tied to military city specialists....
you have to make decisions: more of food/hammer/gold or military?
The game already forces you to make decisions about the allocation of resources. Hammers spent to build units are hammers that can't build a library or theatre. Gold used to support units reduces your research and/or culture rate.
The result? A military strategy is
more powerful, not less. The Civilization which has a focused, militant plan wallops the civilization which is trying to balance culture/research/infrastructure because the latter cannot square off against the former. This is how humans beat up on the AI.
It's also worth noting that, even under the current system, one must strike a skillful balance. AI-Montezuma might be dangerous early in the game, but he stinks over the long haul.
rysmiel -
Re-enable the diplomat/spy unit bribing function
Scilly guy -
I think the addition of assassination units/sabotaging units as spies missions would help.
I dislike anything that takes the game "off the board". At its core, Civilization is a mapboard game. The chart-interface Espionage screen is annoying enough-- adding more importance and more elements to that sort of thing would diminish the value of the visual interface as the game's strategic center.
V. Soma -
war as a too simple way for victory
rysmiel -
The way I would prefer to see Civ 5 handle war being too easy is to make other ways of winning stronger and better capable of defeating military power.
No question that going to war is the optimum strategy for beating the AI. I definitely see your points, both of them. However, rather than addressing war in general, I'd like to point out some more specific factors that contribute:
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Higher difficulty levels give the ambitious human player no choice The AI advantages at Monarch, Emperor, etc. are heavily front-loaded, preventing the human player from establishing an equally-viable empire peacefully.
One solution is to fix the front loading. Eliminate workers, scouts and techs from the AI advantage and instead give them even better production & research rates.
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War is a great way for solving conflicts with your neighbors Again, the presence of effective-but-peaceful tactics like espionage and cultural borders drives up the importance of war. Playing against an advantaged AI, you cannot produce equal cutlure
and equal spy points
and defend yourself from Alexander's advancing Phalanxes. Only by beating down the AI militarily can you overcome all three obstacles.
I'm not sure what the best solution is, but I think it should be easier (somehow) to protect your cutlural borders. Perhaps more weight should be given to distance from city, or how long the city has been there. What I would
really like is if you could go to war and win a tile without having to conquer a city.
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Kill or be killed The cost of losing a well-developed medieval city
and then retaking it is utterly ridiculously high. Yes, cities suffer damage during war, but they do not take centuries to recover! The human player simply cannot afford the possibility of losing a city, even for one turn, so (again) the mechanics drive him to an aggressive strategy.
Simple solution: Allow buildings to "recover" the same way culture does when a city is recaptured by its original owner. Perhaps also do something to prevent the stoopid AI from whipping/starving the population from 16 to 1 over the course of seven turns.
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Resource allocation (a biggie) How many wheat farms does it take to make +1

in three cities? One. How many wheat farms does it take to make +1

in fifty cities? One.
Be it copper, gold, stone, fish, or whatever, the bigger empires just get more and more diversity of resources without ever running short on supply. Again, this drives a warmongering strategy to acquire health, happiness, and strategic resources.
Solution: Overhaul the resource/health/happy system.
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Early conquest provides huge future payoff in full-length games (The biggest biggie) If you want to win a Space Race starting from the Ancient era, you start by going to war. But try it with a Modern start and see if it's so useful.
This could partly be addressed by placing more limits on the size of an empire during earlier eras. The Rhyes mod does this with its Stability function and with civs that crop up during the course of the game. The limit is historically realistic, as governing was more difficult without modern transportation and communication. The Roman Empire was considered huge, but its peak land area is exceeded by six modern nations. The Mongolian Empire was bigger, but proved too big to endure for more than a generation as a whole.
EDIT: *
Scoring system favors Domination A minor point, perhaps: When you play for domination, you're "double-dipping" on the score. The same actions which let you finish sooner also add to population and land area. Got a lot of culture when you built your spaceship? Sorry, no reward.
Twenty-seven cents? Sorry to ramble.
Cheers,
J