Setup program reads directories present in its installation folder and treats them as if they were mods, no additional directories present = error.
Also it makes backup of all data it overwrites and automatically restores it if you untick checkbox next to installed files (you might need to manually delete advice-related files if your mod doesn't use them) - evan if en error pops up backup function will work.
If you uninstall this mod it'll delete all of its own files (3 files in main directory plus g5 folder), if you want to uninstall previously applied AI, you need to untick relevant box and then uninstall.
More info here: http://www.twcenter.net/forums/showthread.php?t=456027 and in relevant section of readme.
There are no issues with TATW 2.1 or submods, initially there was one connected to setup file, but it was corrected a few days after release.
The only current problem is MOS using different versions of my scripts and thus requiring altered setup files (I posted an update for 5.2).
Also if you install a mod in a custom folder changing one entry in one text file will be required - assuming that someone posessed the ability to install in non-standard folder it shouldn't be problematic.
Regards