I was a bit concerned about Gatekeeper but it's turned into a non-issue. Not sure what you mean about subfolders, unless you're talking about the issue with iCloud documents where you can only create one folder, no subs? I think I've saved one doc into iCloud as I only have one machine, I use Dropbox for everything basically.

I skipped Lion because I'd heard so much bad, I like ML though, it's pretty solid.