Awesome!
I'll test it (as soon as I get home) and try to manually fix rails and road texture.. and probably I'll try to re-create animated material for water
About new feature you could add.. maybe a gui for what I think could be useful..
The idea should be a simple switcher for the interchangeable zones that automatically replace the interchangeable mesh during the export..
A bunch of choice that let you chose which version you want to export (for example : Balamb garden "on ground" or "crater" )
We should list all the matches between interchangeable pieces (I can help whith that I guess)
I think this function could be useful for future modding
[Update]
For water texture it's been easy but... rails and road is not..
I'm looking at their UV and it makes me think they should be 256x256 texture like the others..
I found some little pieces that seems to match whith the UV groups but I have to guess exactly where to place each..
[Update 2]
This is time consuming but my theory looks to be correct..
pieces of rails appear to be scattered in wmsetus file.. I'm manually rebuilding the texture for it :