Whenever you're in a dome in the future area, there are clouds in it. And those are black without transparency. Admittedly, you can turn off layer 3 and play that way, but it'd be frustrating to keep having to go into the menu to turn it on and off every time you want to speak to someone (text shares layer 3). Unless a special game hack could be implemented that allowed layer 3 to be left on in the region of the text box, and off everywhere else (sure it'd look dirty, but it'd be a lot more convenient). But whenever you start getting into the region of specific game hacks, you're always talking about trouble (long cluttered menus and a lot of extra work, usually, methinks).
Plus, of course, it just looks so much nicer with...
Only game iirc that actually *needs* transparency is FF V, since when you're underwater in the ship's graveyard, it renders the terrain *and* the water (that needs to be transparent) on the same layer - so turning it off leaves you as a character walking in a maze with invisible walls and no obvious exit.
I'm waiting for Opensnes and even for 0.3 
