Why make appdata the default directory (for windows) when even GAE uses the user directory (c:\users\YOUR_NAME). Appdata is a hidden folder, so fine if the files aren't meant to be touched, like cached files, autosaves, etc, but with Glest's modability, you'd expect that people should be able to find where to place their mods and such easily. Yet, appdata is a hidden folder, a concept that can confuse those without much computer experience (many people have no clue what a hidden folder even is, which, in a way, makes sense, as you don't normally see them and more often than not, they end up being something you shouldn't touch).
The way I see it, there's no advantages appdata has over using a separate folder (eg: "megaglest") in the user folder for windows (linux can stay as it is). Looking at most of my games, most of them (and all of the ones that are modable) use a folder in the user folder or documents folder instead of appdata, and looking at one example (Civ 4), it even provides multiple shortcuts to where specific types of mods (and other important files, like the settings file) are stored. I think this approach would be best for megaglest. I may sound like I'm ranting, but I simply am trying to look out for the new players, to whom glest and its large amount of customability is always daunting, and no need to make it more so by hiding the folder (how likely is someone who never played megaglest before and just downloaded and installed it, and is now looking for the settings file (the INI) likely to find the correct INI? Since the regular INI, which you now state should never be edited, is easier to find than the user INI...).
Don't most/all of the MegaGlest team use linux anyway?