Even if I count only Shounen mangas, it probably goes way beyond 1000. I don't even know what staggering amount, the number of mangas in the world can be and not to forget, that you need to multiply all those numbers by amount of characters in each, to get a proper mangaverse.
Most characters from Marvelverse may be OP but the mangas verse is simply way way larger. Even if you single out, only strong characters and merge DC with Marvel, I think the mangaverse still got the numerical advantage.
Seriously, this sounds like an endless battle; though in my eyes mangaverse would win hands down...
Still, to make a versus-thread, you need to estimate the battle number forces; atleast make it like 1000 strong characters from Manga v/s Marvel.