For me, it's a generation thing. I have reason to believe that the Pokemon Company would not just want to promote Generation 1. Should Mewtwo return and there is no way presumable to use one Mega Form without slighting the other (since each version can only take X and Y respectively), they need a way to represent another generation. Jigglypuff is probably still in, so that leaves one slot. As much as I love squirtle, I don't see how pokemon could go all gen 1. Should there be another 5th rep, then I wouldn't replace pokemon trainer with another pokemon trainer, and give that slot either to Lucario, a gen 5 rep, or an unknown gen 6 rep. So that's my thoughts on the matter. I don't think he is likely to be cut, but I'm predicting based on the knowledge we know. And it's always stuck out to me that Pokemon Trainer instead of Red.
One, why would Trainer be the one to go if a new Pokemon character had to be added? Why wouldn't the one who was prioritized last last time (not counting Mewtwo), Jigglypuff? There's really nothing to say she'd be prioritized above the Trainer this time. Sakurai has obviously shown which one gets priority.
Second, assuming they can't get Mewtwo's forms to their liking, what's stopping them from implementing MegaLucario? Or MegaCharizard?
Third, the Kanto starters seem to have quite a lot of focus in Gen VI, being that you can actually get them from a Professor in the game along with the new Starters. Even if they weren't already the most iconic starters, this helps secure their important to the series, both old and new.
Fourth, it's not like there's an incredibly deserving new character GF is promoting this time around. They're not going to throw in a rather arbitrary character that isn't even being used in promotion over Pokemon Trainer, who by the way will be seen more in current promotion due to that anime coming out that focuses on Red (who is pretty close to the Trainer).
Fifth, GF has shown to not care about representing every gen in the past. In Melee, they didn't press for the inclusion of a 2nd Gen, they were fine with Mewtwo, and Sakurai just added Pichu because he made an easy clone. In Brawl, they were obviously fine with the first gen getting
three more reps instead of Gen III getting anything.
Considering all the veterans have current importance as far as promotion is concerned (Jiggs to a lesser extent - but the Fairy typing doesn't hurt), it's entirely likely they won't press for an actual "newcomer" considering there isn't a clearly qualified one, and even if they did, there's no guarantee (in fact it'd be unlikely) PKMN Trainer was the one of the four Brawl vets to get the boot.