Here's what I think will be good candidates for Final Fantasy characters in KH3D:
First of all, I think IV, V, VI, and XIII are most likely to be represented in KH3D since they all have had or are preparing for recent updates. (IV with the Complete Collection, V on PSN, VI on WiiVC and PSN, and with XIII-2 underway). Of course, by that logic, other Final Fantasies could become candidates if they really are going to do HD remasters.
I think Cecil from IV could actually teach Riku a few things about safely using both light and darkness. That would really go along with the theme of the game being MoM exams and learning to trust. It would also help to improve Riku as a fighter and a person and just build his overall character. I can imagine the scene now. Yen Sid would send Riku into some kind of mysterious dream world where he will encounter Cecil in dark night form, who will engage him in battle just to test his power and will. Then, when Cecil deems Riku worthy, he will go into paladin form and teach him about light and darkness.
From V, I'd like to see Gilgamesh as the new superboss, taking the place of Sephiroth. I find it very hard to talk about Final Fantasy without mentioning Gilgamesh. As many games as he has been in, he is like the very essence of Final Fantasy.
If there is a new circle of Disney villains working together like in KH1, I think it would be nice to include some Final Fantasy villains. That would really liven things up and make the game feel more fresh. Kefka from VI would be a nice addition to the circle as well as Ultimecia from VIII and Kuja from IX.
As for XIII, I think Lightning and Hope would make good allies. As a matter of fact, I think it would be cool if (just for KH3D) they replaced the usual group of FF allies (Leon, Yuffie, Aerith, Cid, etc) with Lightning, Hope, Terra, Zidane, Snow, and some others. This would really freshen up the game and make it feel more new. I think its a shame that most people who just play KH casually and aren't as deep into it as us, believe all of the recent games including Birth By Sleep to be inconsequential spin-offs. While most of them are spin-offs, I don't think any are inconsequential. Adding more new faces and cutting out some old faces would really drive in that feeling that this is a main title.