I think Naruto-kun and Sasuke-kun have reduced HP or defense. That seems to be the best explanation I can offer for the increased damage. EDIT: It also includes damage courtesy of Youmu.
How do they compare? Well, they can be annoying to fight, mostly with their teleporting and projectiles. The big one are some of their more powerful attacks - they don't use 'em too much, but the transformation attacks are a pain in the rear to deal with. Another really annoying attack (though one that Naruto very, very rarely uses) is his Multi Shadow Clone Jutsu, where he summons like twenty clones. I've had a survival or two end that way. They're kinda cheap, but not the cheapest characters I've ever fought.
I'm probably gonna fight the HD version by Youkai as well.
Thanks for the complements!
The Good:
1: Being able to recreate battles within the engine, or having crazy new battles occur.
2: Discovering new characters and series (Tsukihime, for example.)
3: The great feeling of finally defeating someone I'd been having trouble with.
4: Some of the cool original characters.
The Bad:
1: BAD CREATIONS.
2: When unfinished glitchy stuff remains so.
3: When something is clearly half-assed and rushed.
4: When creators get butthurt over the fact their stuff isn't good.
5: Hate characters in general.
6: Not including a movelist. Yes, I can go into Fighter Factory, but that's not what I want to do in order to know how to do a special.
There's good and bad with regards to both of them.
There's good characters, such as ShinRyoga's Mario, the DBZ Z2 characters, and Alexei's Naruto characters, but there's also bad characters from both, such as Ax's characters, anything by S.Nara, and a whole lot of DBZ characters.