Also the issue of how she became Universal World Leader so soon after resurrecting/shielding/purifying everyone when she could have done something to prevent NEEDING to resurrect/shield/purify everyone rubs some people as uncharacteristically power hungry, especially for a girl known to, A, not want to have power or responsibilty, and B, be willing to save everyone and get the best possible ending even if it kills her.
Really, there's nothing WRONG with Crystal Tokyo per se... if the one in charge was one of the uber-pragmatic Outers (I'm suspicious of the "purifying" thing, but only because I'm paranoid, it almost certainly referred to eliminating some sort of demonic taint.) But something smells fishy when the idealistic and self-sacrificing humble messianic figure goes with a plan best described as "not the best, but the most likely to work out very well" that coincidentally ends up with her ruling the world, rather than less likely to work but less status-quo-shaking and less harm-and-stress-to-innocents plans.