A minor thing, but something for the modders. I don't know if this is how you do it already. When you wipe the mod or installation folder, the "user approval" should be a yes/no but there may also be a third option, ignore.
Basically, for the common user, it makes sense to be "strict". But wiping a modder's mod or installation directory could get you some very angry letters. It's where we keep our mods before release after all. So the mod manager should ask for user approval to wipe installation/mod folder, but if the player selects "ignore" it proceeds with the installation anyway, it just doesn't do the wipe first.
Hm... I'm having trouble explaining myself properly.
User decides to install a mod.
Program asks: Warning: You must wipe the /mods/ directory in order to proceed! Do you want to do this?
Yes - program wipes and proceeds
No - installation is cancelled
Ignore Warning - Program does not wipe, installation proceeds
Another suggestion, in the mod "description" window you could also have text that describes dependencies and incompatibilities. So the user isn't surprised when some of those boxes suddenly get ticked in. Although I guess technically there's nothing stopping us from putting that in ourselves.