I got one that I want to see, because it logically explains something I've seen used maybe two or three times so far in pretty illogical ways...
Superman.
That's right, Superman.
When he came back from death, he got a massive dose of Krytponite radiation poured through the Eradicator's body. Because of this his powers came back, but they went haywire, and he just kept getting more and more power.
He bulked up until he looked like the Hulk sans the green skin, he couldn't control any of his powers properly, his heat vision and X-ray vision went off without warning, he couldn't touch anything with destroying it, and he eventually segregated himself from people to keep from destroying everything in sight.
Eventually, he fixed the problem, but... let's send him to the Naruto universe just after that happened, instead. He accidentally destroys part of Konoha, the ninjas come down on him and manage to keep him from just flying away (energy attacks can have an effect on him, so it's not impossible), and the Yondaime seals him into Naruto.
It can go two ways, here, that I can see...
1) The excess energy that was screwing the Kryptonian up could be shunted into Naruto's body, warping it and turning him into a Kryptonian with Superman sitting in his stomach more as a 'guide' than a power source. Eventually he lets Supes out, who flies off to find a way back to his home dimension.
2) He sits in Naruto's stomach as a guide and a power source, eventually he lets Supes out, who flies off to find a way back to his home dimension.
Personally, I'd rather see the former version... especially if it took years to make all the basic changes to his body. Going with that, he wouldn't be super until he was fully changed and charged... it'd be like a gradual increase, over time. Kinda like the ways his powers were in Smallville... they were weak (relatively speaking) and got stronger.