I'll justify my choices tomorrow. 4AM isn't a good time to defend controversial ideas like May or Original Smash characters.
I don't think two Sonic characters is unheard of (especially with Sega seemingly backing up the Wii U like it's their own console), but I don't see the same happening for Metal Gear. Also, as said by others, there's way too many third parties on there either way. Still no Pac-Man, which I think is a bit odd.
Your starting roster is also lacking in the retro department. Sakurai said he likes reviving old series, we can assume there will be a revived retro in Smash 4.
Waddle Dee and Masked Man are fine picks, but fairly unlikely. Kirby is fine with the top three characters and Earthbound is often called 'over-represented' already, a third character would make matters even worse. I would be fine with both of them, but many others wouldn't, I guess.
I'm not a fan of Paper Mario and Toon Zelda on there - both of them would be fairly clone-y and I think there's more interesting picks.
Hoenn Trainer and Micaiah are just plain unlikely to me - Hoenn Trainer would replace Red - and thus toss out three fine movesets for thee new ones which I don't see happening - and Micaiah missed the boat.
Starfy and Andy are pretty original picks (and original characters), but I can't help but feel that they'd step aside for the bigger guns: characters like Palutena, Takamaru, Mii and perhaps even Tingle.
All in all, this feels more like a fan roster rather than a prediction roster..
Here's my prediction for a 45 character roster:
All characters from Brawl included.
8 Newcomers (King K. Rool, Ridley, Palutena, Little Mac, Krystal, Bowser Jr, Isaac and Mega Man)
2 Returning (Roy and Mewtwo)
Bowser Jr, Krystal and Palutena might be pretty risky, but I feel that they each at least have a reasonable chance.
For a 45-character roster I think it's pretty cool. I think you could do without Krystal though - and replace her with a retro character, I reckon.
Finally decided to get that roster creator program.
I'd be very sad if Sakurai decides to pair up Diddy and Dixie. I don't think it'll happen either - we got used to Diddy alone, I don't think that'll change. Other than that, I think it's fine - never played Xenoblade so I'm not too sure how similar Isaac and Shulk would be, but I think it could work