If you're trying to correlate this with the anime, then I think you're forgetting that games =/= anime. They're kind of like in two different universes, if that makes sense. Only one of a kind can exist in the games, I believe (I can very well be missing something but that's the general thing with legendary Pokemon).
I don't think it's "stupid" to be genderless in any case, but hey, one person's opinion.
Well I just assume that the mewtwo that we saw in gen 1 isn't the same we will catch in gen6
I assume the 3 shiny dog pokemon are diffrent than the one we get in game
I assume the heatran and cresscilia we get in gen 4 is different than the ones we get in gen 5
I assume the spirit trio from D/P are different than the ones we see in BW 2
I assume the regi trio we get in gen 3 are different than the ones we can get in gen 4 and in gen5
I assume the bird trio we get in gen 1 and 3 are different than the ones we get in gen 4 Platinum and the remakes
I assume the main legendary pokemon we get inR/S/E are not the same as the ones we get in HG/SS
But hey maybe the games don't correlate with other games so I can be wrong
Oh and since you couldn't understand the first sentence , it basicly ment the no pokemon had genders in generation 1. I understood why they changed it. So I figure since they are restructuring part of the mechanics this gen why not the genderless