There is nothing influential about Roy. He was chosen for SSBM to advertise his game before it came out, and FE6 was hardly a major evolution for the series - if anything, it was a step back. Ike has been a major character in two games now (yeah, he's in GoD, and pretty important oo), so if anything he's more important to the series than Roy is. You say that most everything FE9 was done in previous FE games, but the same could be said about FE6 - the only thing FE6 added was supports, which is just a different and not necessarily better version of FE4's lovers, and it stripped a lot of cool things out that FE5 had.
However, even though I don't want Roy to return, I think "but he wasn't that good in SSBM!" is a poor argument. Fox was merely decent in SSB, and Kirby was awesome - both of those things changed.
Marth is historically significant to the series, but I personally don't like him, particularly his character design. And let's face, his games simply aren't very good today. If it were up to me, I'd get rid of him.
I would also like to see a mage. I think it would be interesting to have a character that has to rely almost completely on magical spells and is very weak in melee, possibly even having spells as some of their A moves.
Personally, I think Sanaki (empress of Begnion) would be a good choice. Yes, she's in Goddess of Dawn, she looks pretty cool, and I hear from people who have played it that she's very important to the story - far more so than in PoR. And unlike Micaiah, who only has light magic, Sanaki has both light and all three elements, giving her a bigger set of potential moves to draw on. I also like her character design (
http://img.photobucket.com/albums/v139/VincentASM/FE10/Nin/dori5.jpg) more than Micaiah's.
So my choices would probably be Ike and Sanaki, and perhaps Hector or Marth as a third FE character.
Of course, I'm speaking strictly on who I
want to be in there. Not necessarily who I think will be.