I believe Civ IV as is is pretty darn good and most things should be kept just the way they are except:
1) Independence of colonies/vassals. Overseas and conquered territories, colonies and vassals should be striving for independence.
The master can choose when/if to release them and should face a realistic prospect of war if not. Vassals should always want independence unless they are very weak militarily - if it is 50% of the master's power, its land/pop should not matter.
If you settle another landmass and you do not liberate it into a colony, it can revolt and start a revolution if it reaches a low stability level (see below) forcing you to consider giving it colonial status . If you give it colonial status, you save maintenance costs and have a chance to avert complete independence. If you decide to wage a war to prevent any form of autonomy, the rebel territory gets 2X the # of population points defensive units and 0.5X the # of population points of siege and cannot build more. If you win against it within a set number of turns (40?), stability increases significantly for at least some time. If you don't, it becomes an independent nation and you can still destroy it, but now it can build units as well and stability will not increase if you conquer them since they were already independent. Building jails and reducing taxation in your overseas territories/colonies can be used to make them happier and dramatically increase stability. Giving them colonial status will increase stability although the colony should start with much lower relation than +10 (maybe +3 or +4). If you start wars, you should get diplomatic penalties like "you brought us into a war". If you even trade for their resources (demand should be even worse), you should get "you are exploiting us". Your relations with other nations in the world should also play a role. If relations are below pleased, a revolution can begin and you have the same options as above. If you have a colony, they can be bribed/motivated by other nations to begin revolting much like war bribes.
Conquered territories should behave similarly to colonies.
2) Corruption. Yes this was in Civ 3 and it was poorly implemented, but I think it's important to include it because it is a big factor in most societies. It should result in loss of the certain proportion of commerce produced in the city. City maintenance should still be there; corruption is extra. Jails, Police State should reduce corruption significantly.
3) Taxation. The ruler should have an ability to tax its people to overflow its coffers although this should decrease happiness and eventually stability. Taxation rates should not have a limit under Monarchy or Police State, but should be limited under Universal Suffrage. People can revolt about high taxations by demanding Universal Suffrage and only large military garrisons/jails can stop these revolts.
4) Stability. Your empire should be unstable after a long war/huge taxation/out of control corruption and pieces of it or the whole thing should be in anarchy or better yet have a chance to secede as a separate nation. Something like the Rhye's Mod. Overseas territories should have lower stability in general.
Stability (separate values for each homeland city, but one value for an overseas or conquered territory) should depend on:
1) Happiness level - increase stability.
2) Corruption level - decrease stability.
3) Military presence - increase stability.
4) Presence of Jails or authoritarian government (Police State and to a lesser extent Monarchy) - should increase stability.
5) Presence of Slavery - not adopting Emancipation should lower stability drastically.
6) Frequent civics changes.
7) Religion - areas with different religions should have lower stability.
5) Permanent alliances should be renamed State Union and result in 2 nations becoming one. Permanent alliances as they are now should not exist as no alliances are permanent.
6) More random events pertaining to new concepts like corruption and instability.
7) No more Ironclads. Replace them with a Steamboat that has 15 strength and 3-4 movement. They would be shortlived as they are now, but offer a significant upgrade over Frigates/SOL and so be worthwhile.
8) No more Airships are Physics. Make them available at Assembly Line or something to avoid them being unrealistically powerful.
9) Maintenance for overseas territories could be reduced a little to counterbalance the tendency of new lands to separate.
10) There should be a light cavalry unit in the middle ages (like an Improved Horse Archer) and Mongolian Keshiks should be a replacement for these. Improved HA should have strength 8, 3 movement points, and Spearmen/Pikemen should only get +50% against these. They should also have increased flanking damage to siege.
EDIT:
11) Religions should be reworked to allow Schisms. Christianity should split into Orthodoxy, Roman Catholicism, and Protestantism, Islam into Sunni and horsehockye, and Buddhism into Theravada etc. Civs with different branches of the same religion should have a +ve diplomatic bonus , but much less than civs that belong to the same branch. If a nations has even a few branches of the same religion, stability should decrease.
That's it.
1) Independence of colonies/vassals. Overseas and conquered territories, colonies and vassals should be striving for independence.
The master can choose when/if to release them and should face a realistic prospect of war if not. Vassals should always want independence unless they are very weak militarily - if it is 50% of the master's power, its land/pop should not matter.
If you settle another landmass and you do not liberate it into a colony, it can revolt and start a revolution if it reaches a low stability level (see below) forcing you to consider giving it colonial status . If you give it colonial status, you save maintenance costs and have a chance to avert complete independence. If you decide to wage a war to prevent any form of autonomy, the rebel territory gets 2X the # of population points defensive units and 0.5X the # of population points of siege and cannot build more. If you win against it within a set number of turns (40?), stability increases significantly for at least some time. If you don't, it becomes an independent nation and you can still destroy it, but now it can build units as well and stability will not increase if you conquer them since they were already independent. Building jails and reducing taxation in your overseas territories/colonies can be used to make them happier and dramatically increase stability. Giving them colonial status will increase stability although the colony should start with much lower relation than +10 (maybe +3 or +4). If you start wars, you should get diplomatic penalties like "you brought us into a war". If you even trade for their resources (demand should be even worse), you should get "you are exploiting us". Your relations with other nations in the world should also play a role. If relations are below pleased, a revolution can begin and you have the same options as above. If you have a colony, they can be bribed/motivated by other nations to begin revolting much like war bribes.
Conquered territories should behave similarly to colonies.
2) Corruption. Yes this was in Civ 3 and it was poorly implemented, but I think it's important to include it because it is a big factor in most societies. It should result in loss of the certain proportion of commerce produced in the city. City maintenance should still be there; corruption is extra. Jails, Police State should reduce corruption significantly.
3) Taxation. The ruler should have an ability to tax its people to overflow its coffers although this should decrease happiness and eventually stability. Taxation rates should not have a limit under Monarchy or Police State, but should be limited under Universal Suffrage. People can revolt about high taxations by demanding Universal Suffrage and only large military garrisons/jails can stop these revolts.
4) Stability. Your empire should be unstable after a long war/huge taxation/out of control corruption and pieces of it or the whole thing should be in anarchy or better yet have a chance to secede as a separate nation. Something like the Rhye's Mod. Overseas territories should have lower stability in general.
Stability (separate values for each homeland city, but one value for an overseas or conquered territory) should depend on:
1) Happiness level - increase stability.
2) Corruption level - decrease stability.
3) Military presence - increase stability.
4) Presence of Jails or authoritarian government (Police State and to a lesser extent Monarchy) - should increase stability.
5) Presence of Slavery - not adopting Emancipation should lower stability drastically.
6) Frequent civics changes.
7) Religion - areas with different religions should have lower stability.
5) Permanent alliances should be renamed State Union and result in 2 nations becoming one. Permanent alliances as they are now should not exist as no alliances are permanent.
6) More random events pertaining to new concepts like corruption and instability.
7) No more Ironclads. Replace them with a Steamboat that has 15 strength and 3-4 movement. They would be shortlived as they are now, but offer a significant upgrade over Frigates/SOL and so be worthwhile.
8) No more Airships are Physics. Make them available at Assembly Line or something to avoid them being unrealistically powerful.
9) Maintenance for overseas territories could be reduced a little to counterbalance the tendency of new lands to separate.
10) There should be a light cavalry unit in the middle ages (like an Improved Horse Archer) and Mongolian Keshiks should be a replacement for these. Improved HA should have strength 8, 3 movement points, and Spearmen/Pikemen should only get +50% against these. They should also have increased flanking damage to siege.
EDIT:
11) Religions should be reworked to allow Schisms. Christianity should split into Orthodoxy, Roman Catholicism, and Protestantism, Islam into Sunni and horsehockye, and Buddhism into Theravada etc. Civs with different branches of the same religion should have a +ve diplomatic bonus , but much less than civs that belong to the same branch. If a nations has even a few branches of the same religion, stability should decrease.
That's it.