Pokemon Trainer
Pokemon Trainer will be coming back in some form, the question is, will he return as Red? I sure hope so and I have a very good feeling about it.
Despite not being as relevant as a 4th gen Pokemon Trainer, Red was selected over Lucas. Why is that? Because he was the most popular and important Pokemon Trainer in the series; being the protagonist of the game that started it all and continues to be loved to this date. It shows that relevancy isn't everything and that importance to the series is the most important factor in deciding characters. He was a decently popular choice for a Melee rep and thinking about it, he deserved to be in that game over Pichu. Screw it if it gave us no 2nd gen rep, at least it would have been great.
With that said, there is no reason for him to go. His only threat is the possibility of a 2nd/3rd/5th gen Pokemon Trainer taking his spot; but this move would cause lots of outrage, moreso then Mewtwo's removal, so I doubt he's going anyway.
90%
Isaac
There is no reason why Isaac should not get in. He would be incredibly unique and would be a fantastic character that would make many people happy. He also reps a popular C-list series. Deserving
While I wouldn't mind Matthew getting in, he has numerous problems with his inclusion. The only thing going for him is that he's the protagonist of the latest game and that he is relevant, which is probably not going to be enough to get him a spot. He has very little fan demand, his game was the worst selling and worst received game in the series (Not bad, but not as good as previous games), and while important, is not really the defining face of Golden Sun. Picking him over Isaac for the sake of relevancy would be a slap in the face for fans who desperately want Isaac in (I guarantee you that fans are more picky about Golden Sun reps then me, so this is understandable). As such, his chances are low.
Isaac is still relevant, was the protagonist of the best-selling and best-receiving game, is the most important character in the game, and receive near unanimous demands for his inclusion in SSB4 (When was the last time people spoke against him?). Icing on the cake, he was an Assist Trophy in SSBB. This is a case where importance and popularity by far overpowers relevancy to the series. Since Isaac has all three and I doubt Matthew will be playable; I don't think it's a question of Isaac or Matthew, but likely instead Isaac or no Golden Sun rep.
80%
I predict 71.22% for Takamaru.