I did a nice little scan, but my friend's being a bastard about helping him with his game so I'll be back when I can with my findings.
Basically Yoshi and Link confirmed, Pikachu and Lucas semi-confirmed. More later!
EDIT:
SO, a few things:
-Meta Knight and Ice Climbers team up, fight on a large Icicle Mountain stage
-Yoshi and Link team up. Link begins in a fiery dungeon, but fights with Yoshi in a watery cave.
-Peach ends up in Skyworld someway somehow. Backtracking with new characters?
-Samus is seen in an area with ruins.
-Pikachu is seen on New Pork City.
-Lucas uses his bat to fight off "evil Pokeballs" (forget the real name): Lucas and Pikachu team up? Ness definitely deconfirmed now.
-Bowser utilizes the same gun as Wario, laugh is twisted
-Primids are seen preparing for war, all equipped with cloneish skills (a few have green versions of Zamus's whip, one uses Mario's Dash A, another has Dedede's hammer)
-Ike fights in a Fire Emblem-esque area (a bridge), with fallen ruins behind him. Next scene shows a door like the DK video inside a FE style throneroom.
-Rayquaza definitely a boss: shown in montage with other bosses.
-Diddy is shown watching the Primid "ooze" form in the jungle, FYI
-Bowser confronts Fox and Diddy at some point, not just DK and Diddy--does DK become a trophy like the captured princess? *thinks we'll see Dark Peach/Zelda and Dark DK as bosses later on*
-We see what happens when Peach is left behind and Zelda leaves with Kirby (pretty much the same
)
-Vehicles confirmed. Link rides a tank that fires lasers at STICK FIGURES. wtf?
And that's all folks. The only characters not yet paired up are:
Ike, Sonic, Dedede, Snake, Samus, Pokemon Trainer, and, despite being villains, Bowser and Wario.
My money's on.... Pokemon Trainer and Dedede (like I originally guessed ;p), Samus and Snake, Sonic and Ike, Bowser and Wario. But a part of me also wants Snake and Sonic to be uninvolved as starting party members, y'know?