First of all, there has to be a Mod, correct?
What we have to agree on first is what civs will be in the game altogether. That includes Civs in scenarios, the actual mod, dungeons, whatever. I agree with Kulade, in that we should definitely have a random game, with at least most of the civs available. We are doing that with Star Wars MOD as well, keeping the feel of a true civ game to a certain degree.
Somethings just cannot be done on a map, but some can.
Example: Termina and Hyrule can be done,
Hyrule and the world from WW should not be, since it is basically the same place, just sunken. It would be best to combine those in a random map.
As for scenarios, there should be a general "defeat Ganon" scenario, that involves collecting triforce pieces, medallions, something like that, probably in the place of the Space Race. We could also include some sort of dungeons, that you have to defeat in order to get to resources needed or something like that. Wars are also a very definite possiblity, such as the war from ALttP, and the one mentioned at the beginning of OoT. We can only guess what they were, but that is where imagination comes in.
I have played only Oot and MM lately, so any information on ANY other civs is greatly appreciated. If you have any, please post whatever info you can.