a way to disable the "new world" code would be nice. right now the mapscript tries its best to place all civs on the largest continent, but I'd rather have them spaced around evenly. since that choice is available in perfectworld I hope it's not hard to add it here too. when I played perfectworld I always turned "new world" off

the "break pangea with a meteor shower" option from perfect world would be awesome as well, for those that like high cohesion but still hate pangeas for example
not an issue, but something I dislike is that even with low cohesion, high sea level, all the continents are reachable by earlygame boats that cannot travel over ocean. this really takes away the usefulness of being able to "trade over oceans" with the Astronomy tech, Sailing it's all that needed. distant continents should be separated by oceans instead of simple coast imho.
oh, and again imho, the code that says "lakes are always less than 10 tiles so that they are freshwater" should be applied to all sea levels instead of low sea level only. otherwise it kinda takes away that "lake" feeling when you have lots of big lakes that are not freshwater
I can understand why you would want to keep the number of options showing up in the main menu low to avoid cluttering the screen, but I disagree, I think the more options available, the better. perhaps it would be possible to have as many options as possible, but have most of them only adjustable through manually editing the python file so that they don't clutter the screen? something that's easy enough to use that you don't have to learn python, just a simple "option xxx = true" in the python file that you can easily edit with notepad would be great. similar to how you can set Erebus to soften peak percent chance, or add wrappings
a couple more features from perfectworld that would be awesome to have here are altitude affecting terrain ( IF it's not in already, not sure

it's great to see higher terrain being colder. right now you see cold terrain only near the pole, but very high altitude spots should have some as well imho

) , and having different resource sets on different continents to encourage trading ( so for example one continent gets cow and wheat, another gets pig and rice etc. )