Although most games are based on others, even the more blatant rip offs aren't usually as close as Neutopia is to the original Legend of Zelda. Golden Axe Warrior comes close and Golvelius is way different as far as rip offs go.
Other than Nintendo not being cool with the whole Zelda rip off factor, they might also not want Neutopia stealing any of the NES & SNES's Zelda games' thunder.
I find that...extraordinarily unlikely.
Why, because Neutopia
doesn't even compare? I'm not saying that Neutopia is way better than any Zelda(
however it is my 2nd favorite Zelda game after the original), but if someone unfamilar with the early Zelda games were to try out NES Zelda for 500 points and Neutopia for 600 points, they'd probably feel like they got ripped off buying Zelda since they're the same game except that Neutopia looks nicer.