Firstly, a job system. But a relatively fixed one. There are so many jobs to pick from, but each character gets to pick one (or two, or three) roles they can use and they must use them for the rest of the game. This makes for incredible amounts of replayability.

Secondly, a distinct lack of time travel. I hate time travel in video games.

Thirdly, at least one character that isn't a humanoid. None of this Fran business. I'm talking Red XIII. Hell, maybe a humanoid that is of absurd size, but not "It's not a human, honest, it may move like a human, be the same height as a human, have the same general body proportions as a human but BUNNY EARS!!! Not human!" I'd like for a tiny character. Even a fairy would be cool, a la Tinkerbell. Basically, these kind of characters are not only unique in their appearance, but also are unique in what you can do with them gameplay-wise.

Finally, a good, solid, thought-out storyline. With a good touch of comedy.

ALTERNATIVE ANSWER: If you have seen FFXIII-2's Sunleth Waterscape Paradox Ending, I want that as a Final Fantasy main numbered game. Obviously not the exact same characters, but a concept along that kind of line would be amazing. Who makes games like that anymore on a AAA scale? Nobody I can think of! Do it, SE! Surprise us! A JRPG with no humans or humanoid creatures would be so, so, so much fun.