A few of my opinions on some things being discussed:
I doubt Sonic and Snake will get cut. I mean, look at the response to the cutting of Mewtwo and all the clones. Imagine cutting two completely unique characters. That's calling for nuclear war. Like Mendez said, nowhere are they stated to be guest characters. They're at the end of the roster because they're third-party, and those characters haven't been allowed into Smash until now. I'm highly confident they'll return.
I'd like to see the second trainer be a female. Perhaps we could give them actual names this time. I know in Ruby/Sapphire, the boy was Brendan and the girl was May. So it's not like we'd have to be dealing with names like Red and Silver. I'm not saying I'd utterly hate that, but face it, the names sound weird. As far as PT2's Pokemon, either three evolutions of the newest set of starters, or a spread combination. If we were to do it now, we could do some from generations 2, 3, and 4, done in various stages like the first PT. For example, Treecko, Combusken, and Empoleon.