Very powerful Xmen team but Naruto has a speed advantage and the damage output these guys dish out is crazy. They also have high end durability...hell, as children they got right back up after getting their face crashed into a mountain. Their versatility is insane as well but I don't think they've ever faced beings that can attack the mind.
They have something similar in the Marvel U, however; chi. All living things in the Narutoverse possess it, it's their life-force, for want of a better term.
If Iron Man were there, though, he would do pretty well.
Of the X-team, I place the most faith in Magneto. Once he gets into the air, and SUPPOSING he stops using his other 5 senses and relies on his EM sensing abilities, he could do well.
Are you all serious? Everything you are saying about the Narutos is true, but are you forgetting who the are fighting?? Apocalypse ate the freaking legacy virus. Four of the five Marvels have psi, three og which are high level. Selene has super speed and would FEAST on their life force! Poccy and Sinister would gasm at the chance to go up against new genetics. No team stomps IMO.