I believe there is one thing that just must to be implemented in any Civ/Col/whatever game: historically correct Earth map. In this case, historically correct map of Western Hemisphere.
We do have several of them, yes, but there are three issues I'd like to ramble about right here.
1 - Positions of Indians. Aztecs in Brazil? Tupi in Canada? I can live with that stuff on random map, but not in Western Hemisphere. It will be so nice to place them, well, in places. Village placement is not important I think, but it will be very nice to roughly put them where they belong to.
2 - Starting positions of Europeans. This is somewhat difficult, at least for several European powers. But in general I believe we may put them in this way:
France - top north (Canada);
England - more to the south (US);
Spain - center (Carribean sea and Main);
Netherlands - further to the south (Suriname);
Portugal - obviously, top south (Brazil).
This still won't fix some very important historical incongruities, such as French Louisiana and Guadeloupe-Martinique; Dutch Curacao and New Amsterdam, Spanish Mexico and English Barbados and Jamaica, for example. But still it would be better than to spawn French to the south of Portuguese.
3 - Expanded Carribean. Historically, Carribean sea region with islands such as Haiti-Espaniola, Cuba, Jamaica, Lesser Antilles was very important place during Colonization of the New World. Unfortunately in this game no one cares about these small patches of land.
Basically I believe that Carribean islands should be artificially enlarged (distortion is not that important) and buffed with unbelievable wealth of natural resources. Like 3 Tobacco and 2 Fishes for Cuban North-West, where Havana should be. It will make Carribean sea the sweetest spot, with many interesting naval action.
Why do I post it here? Because AoDII is basically new "default" Colonization in my opinion. Couldn't care less about Vanilla or some scenario not compatible with AoDII.
And while issue #3 is actually in my power to solve, I have no idea how to fix issues #1 and #2 in proper Scenario format, where you still can select your leader, not only your nation with preselected leader.
If anyone would point me into general direction of some guide describing how to do this, I will definitely volunteer myself into making of the historically-correct and fun map of Western Hemisphere, which I think this game still lacks.