Team Captain N
Princess Zelda instead of
Princess Lana, Simon Belmont, Mega Man, Pit, Duck Hunt Dog instead of
Duke, especially since DHD has target based smash attacks, and a clay disc, which I'm sure reference to the NES Zapper. And of course, Samus, because I thought for sure she was in Captain N at one point. It's been a long time since I've watched that cartoon, though.
Team Retrospect
That's not to say that there aren't plenty of retro characters that should fall within this team. Your average American or wherever you live probably wouldn't know where the Ice Climbers or R.O.B. come from. Possibly the same with Mr. Game & Watch. Again, any retro character could fit in this group, but for the sake of it, I'm putting these four together.
Team Bound Together
Alright, it makes sense for Ness and Lucas to team up. Where does Pokémon Trainer fall into this? Well, because of Mewtwo. And if you've played EarthBound Beginnings, you'll notice a particular character that Mewtwo closely resembles if you get far enough.
Team Reptilian
I didn't include Ganondorf here, because of how he treated Bowser in the Sub Space Emissary. It wouldn't make sense for them to team up again.
Team Future's Past
I don't know the current Zelda timeline, but obviously they're all Link from different eras, so why not?
Team Focused
They're all fit, they all must focus during battle, and I just think this team would be interesting to have together.
Team G-Diffusers
No real connection here other than that all their vehicles use a G-Diffuser. Also, James McCloud looks like Fox's dad.
Team Darkness
Who is the leader of this group, anyway?