I can see this as being an Evangelion fanboy's ultimate side story fantasy. The whole story is even constructed like an alternate universe fan-fiction. While the characters' appearances and, to some degree, backgrounds stay relatively unchanged, there are some notable differences in their roles in this story universe.
Nerv isn't a top-secret government agency anymore. Instead, it's a Catholic school for the elite. Rather than being the emo that everybody hates, Shinji takes on the role of a typical shounen protagonist who gets unknowingly sucked into the conflict of supernatural forces that could determine the fate of the world. Kaoru's still a little creepy, but he's sexual orientation seems far less ambiguous this time around. Rei is still the silent enigma, and Asuka doesn't even get that much exposure in the first chapter. Misato is given the role of the "hot teacher," while Kaji acts as Shinji's irresponsible guardian.
Casting choices aside, the first chapter suggest the story won't be deviating too far from the standard shounen fare of "young heroes kicking bad guy ass and saving the world." I don't really have a problem with that, but it's a little bit unsettling seeing Shinji acting so... normal. To be fair, though, the story still has a lot of room to develop, so I'm hoping for some surprises.
Art wise, I'm digging the clean, crisp presentation. The style is significantly different from Sadamoto's designs, but still captures the essence of the characters. No complaints here.