This is a bit pie in the sky but i figured i'd put it all down on paper just to get it out there:
I'll take them one at a time.
1. Tidal Estuaries/Canals. One is natural, the other is a tile improvement. The essence is that it'd allow navel units to 'move up river. Obviously, for the former, it'd have to be a part of the map and not a part of the script, unless it was hard-coded (or whatever it could be called) that for a whole river's length (be in 3 tile-edge-lengths or 30), a tidal estuary constitutes 10-25% of the bottom of it, making it possible to build cities 'inland' that still had connection to the 'coast' and allowing both navel and land units to occupy the same type of land tile. I think this would add tremendous depth to the game.
2. <2nd City Type> - call it a castle, a military base, an outpost, or whatever; it'd occupy a single tile, and would perform many functions of a city but it wouldn't grow in size, would have a base production that could only be improved upon through limited construction tree, and it would not grow outward in culture. The reason for this is that for players who like to expand frontiers, it doesnt make much sense to have the heart of your empire the strongest point - i want to be able to fortify my boarders. Citadels and Forts are good and fine, but i want a more durable structure of permanence.
3. Completely overhaul the nature of resoruces. Strategic and 'generic' resources would be a lot more common, luxury resources tremendously more rare (but provide a double or triple the happiness benifit). Strategic resources like iron would be found in a maximum alotment of 3 or 4, uranium in 1 or 2, aluminum in 1 or 2, oil in 2-4, etc, instead of huge windfall lots of 6, 8, etc. The presence of this unbalances the ability of the ai to produce a ton of potent units later in game. By making the resources more common but weaker in tile-concentration, it'd greater balance the progression of the game and the way to ai builds (at least, so i have infered). But this is something done on a map component.
4. Perfectworld3. I am in love with this mapscript, but for all of its greatness, i have found flaws that i feel like should be able to be improved upon. Customizable continent size, the propensity for 'single isthmus connectors between huge continents' and the general customizable notions like sea level and 'rugged' features.
Anyway, i have no idea how to mod anything. i tried to change small things and ended up having to uninstall and reinstall everything because it screwed it up. But i would love to be a part of the continuing brain trust.