To go with the afore-mentioned Final Fantasy, Kingdom Hearts would also be good. Or include it as an expansion set.
As for other franchises, it's tough to say. If LotR doesn't have one yet (though I bet it does) that could work. Just imagine printing only ONE copy of The One Ring - "one card to rule them all!"
It would also be hilarious to make a Madden football CCG, maybe using already-printed football cards, and then see frat boys across the country moving cards around on a table like they're playing Magic.
And before you laugh it off, hear me out - if you take the Archie comics / SatAM continuity, I think Sonic could work, too. There's enough characters on both sides, items, and other stuff to make it work well.