its marvel hands down and if you need me to list why ok
The only real chance that the Naruto universe has would be to unleash all 9 Demons that were the original scourge of the world. That aside, I'd say the villages actually have a decent chance against moderately powered/non-powered characters. Ultimately though, MU 616 curbstomps the Naruto-verse.
Odin alone changed the universe with a wave of his hand while Dr Strange can put all demons in bottles then drink em for fun.
If all else fails the Punisher will find a way to kill every frickin' ninja in the series, even if all he has is a toothpick and a malfunctioning table fan. If he dies, Deadpool can take over...and he's banned from dying.
forget Naruto, even Marvel's ninjas can do him in, no sweat. Even Jamie Madrox has to have a ninja dupe in him somewhere....
that is not contest, that a simple B***h slap on naruto. really maybe 20 odd character, against over 60 years worth of characters. maybe to make thing fair would be to use a team against them. like x-man, S.H.I.E.L.D, Avengers, Defenders, and so on. and even if you did that, Marvel still wins hands down. hell Daredevil alone could take down like 5(+) naruto characters.
Overall the Marvel Universe would Curbstomp the Naruto Universe.
However, Daredevil wouldn't be the one doing much of it. He has fighting skills, try putting that up against a kid who can survive a fist smashing through his chest and if in a real pinch (against some of the tougher street levels) Could release the 4th Tail and let Kyuubi take the wheel, or use the Rasen-Shuriken and pretty much cut all the celluar bonds of the enemies. Hell, all that Naruto Universe would have to do against him is send in the Sound Ninjas, not even the Sound 5..Zaku Kin and Dosu..Yeah the 3 Genins that were Sasuke's punching bag.
Marvel would win, but with heavy Casualties unless they bring in the big guns at the start.