I can only speak for myself, but I generally only play a custom map once to completion. Hence some lazy usability sugestions
Could the custom maps screen allow for the deletion of maps (click and hold brings up a delete OK/Cancel msg box). This would help keep game memory usage to a minimum as well as stopping the need to keep navigating to the maps dir.
A real "nice to have" is once a custom map has been completed, there is the option to delete the map on the win screen.
Another "nice to have" would be the ability to store custom maps in My Documents/
path name. This would allow more use of the "send to my PocketPC" and other Windows funcationality and hence not need to navigate to the dir structure to install custom maps.