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Havok
Polaris
Iceman
Gambit
Rogue
Wolverine
and I'll arbitrarily add Colossus

vs,

Mach IV
Speed Demon
Radioactive Man
Atlas
Joystick
Blizzard
Photon (Genis)

Genis was just "re-born" so his powers are kind of whacky, and he hasn't fully explored them again, so he can't just wig out and smack them all down easily. These are both teams comprised of people at difficult cross roads in their house, check out the Golgotha arc, and the recent Thunderbolts issues to see that these teams are having tough times, and I'd like to see them face off.

Iceman and Polaris will make things really hard for the Thunderbolts.

But Radioactive Man and Genis-Vell are no pushovers either...

I'm going to tentatively say X-men for now.

Rogue will fry Blizzard with her new fire powers and flight.

Havok will put Mach IV out of comission.

Joystick will get diced by Wolverine.

Since his ressurection and upgrade i'm pretty sure Colossus will put the hurt on Atlas.

Iceman will have to take the heavy load. He is going have to keep Radioactive man at bay.

Polaris versus Genis-Vell? Depends on how pissed of Polaris is and how much of a downgrade Genis got.

I really like both teams; it could go either way.

Genis didn't get a downgrade, his powers just changed a little bit, so he hasn't adjusted to them yet.

I think Atlas can take Colossus, Peter's stronger than ever now, supposedly, but Atlas' ionic energies have further strengthened him recently.

And I think Mach IV can take out Havok, he's got a super edge in maneuverability, and has great offensive abilities with his suit.

I don't think Blizzard and Joystick will last that long though. Could go either way, like you said.