Wrong section O_O
Honestly, the naruto universe has far more power on its side (in both numbers and abilities).
The main (combat) characters of FMA (Al, Ed, Ling, ect.) could easily beat some of the lower/mid tier characters in Naruto, but when it comes to the upper tier Naruto characters (which there are a vast amount of), the only FMA characters that could honestly last against them would be Roy Mustang (due to his flame alchemy which is clearly a most troublesome skill to fight against combined with his newly acquired ability to form transmutation circles without an array), the Homonculus (due to their regeneration and other abilities which may would prove tasking for most of the Narutoverse characters--though the regeneration remains the most difficult to deal with), Van Hohenheim, and Father (Hohenheim and Father are truly the only two characters that I'm confident could trump most of the characters in the Naruto for obvious reasons.)
But overall, with the Kages, Akatsuki, and all of the powerful ninja from each village, the FMA universe stands little chance O_O
Then again, FMA has guns xd