I downloaded ver .21 and it's got some great potential. I think the main layout of the app is pretty much in focus now.
1) I would consider making the Generate Misc to be resources and not the Polar caps. The Polar caps could simply be an off/on check box. As for I am concered. Others might disagree though.
2) I love the X\Y Wrap, that feature this will be very nice for ensuring the map is playable in a round World based game.
3) I wouldn't worry to much about the size. With such a customized map I think the upwards of 150x150 is enough.
4) Can't wait for the mountains and forest to be generated. I think is crucial to be able to see them on the preview. Like you can the desert. Different colors of course.
5) You might do away with the number of islands box. The number of continents and number of islands are kinda one in the same. One or the other would work fine. The purpose of either is straight forward.
6) The speed of map creation and randomization is very impressive! Scary considering how long Civ4 takes to load them.
I can't comment much on the coastal features. I don't know if there up an working yet. I tried several different maps and didn't notice anything different between the types.
Don't forget Forest Ratio on the Terrain Tab!
Curios what the Terrain-Desert\Plain shape and Hill\mountain shape values will do.
As for rivers. I know there needed but I don't think it will be possible to view them on the map preview. Not a bad trade for a totally customized map. Unless of course you can think of a way to put them in.
I know there's a lot to digest.
All in All - All things said

you the man!
TBear2520