I don't think 18 years will do much for Greninja.
Squirtle and Ivysaur will forever be the first starters, and that's not going to change. (Heck, they even gave them a 2nd go for starters (3rd if we count Fire Red and Leaf Green) in Pokemon X/Y.
NO one gave 2 flips about Ives until Nostalgia shades were thrown on and SSBB. Time changes people's opinions.
Greninja will have at least 8 more new popular starter characters ahead of him by then. He'll be no different than say..Samurott.
Also, who's to say Pokemon Trainer can't get in as an ACTUAL fighter, and not be limited to the background?
Since the circumstances are completely different, you shouldn't be comparing the two. IN Pokemon, most trainers were shown to be sitting in the background giving orders (Chuck, Bruno, and Marshall I believe the only ones to try and show their physical skills. Didn't include the anime as the anime is written for dunderheads (us as kids) and isn't that great of a source). Being summoned to attack like a Phantom Knight sounds silly and shouldn't be implemented.
Zelda has a summon-type special move, PT could easily do the same, except with all specials.
That would mean more work for Sakurai and be a slow way to attack if ALL the specials were like that.
YES I know that's highly unlikely seeing how Charizard is Red's iconic Pokemon and trump card. (That'd be like taking out Dark Magician from Yugi's arsenal). But in the manga, Bulbasaur was his starter. And he might get the Squirtle/Bulbasaur/Charmander starter pack, MAYBE along with some others to help him recover, such as Pidgeot.
Anyway, I don't mean to bring back too much hope. But where there's a will, there's a way. If Sakurai considers the Trainer (Red) worthy, iconic, and important to both pokemon and ssb, he'll bring him back. And if he couldn't due to Game Farts, well, at least he tried.