Okay, seriously guys? We're talking about the huge pop culture that is Anime and all you guys can think of is Bleach, Naruto and Dragonball, and maybe some less mainstream anime???? Let's have some real anime characters to work with!
Merry Nightmare from Yumekui Merry -- Gatekeeper between the Dream World and the Real World. She can also tear down the very gate that she protects and wreak havoc on both sides.
Black★Rock Shooter -- This girl could be made out of solid iron for all we know. She can survive being ground by metal blades, stabbed through the heart by an oversized lance and take being shot at like it's nothing. Also, have you seen the size of the gun that chick lugs around?
Yaya from Unbreakable Machine-Doll -- She uses magic, martial arts, defence and speed, all of which could be used to wipe the floor with her marvel/DC opponents.
Characters from Nichijou -- So random that anything can happen.
Aiba Mui from Magical Warfare -- She has a magic gun, so as long as she aims, most Marvel characters are dead.
Fear Kubrick from C³ -- Yandere-Tsundere-Deredere torture device from the Inquisitions manifesting as a girl, over 500 years old with as much experience in combat, also equipped with 32 mechanisms of torture. Also has a tendency to go beserk.
Eucliwood Hellscythe from Kore Wa Zombie Desu Ka? -- Can kill literally anyone by saying "Die" -- unless they're already dead. Doesn't work on...
Kanade Tachibana from Angel Beats -- Her Guardskill: Distortion will deflect any attack and Delay allows her to evade any attack. She also has six swords in her arm and can replicate herself.
And lastly:
Shana Nietono from Shakugan no Shana -- She's a Flame Haze who can stop reality and kill whoever she needs to instantly before replacing them with Torches. She could kill Superman and take his Power of Existence without breaking a sweat and Superman would not even know it was happening. He'd be a torch, with his power gone and left with a lifespan of several days before he disappeared.
There are tons more characters out there who can trash America's superheroes, all you have to do is find them. Don't just rely on Goku and Naruto.