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They made Victini Unova's number 0 because they were really pushing it to be used in-game after the player reaches Castelia.
Since it was technically an early game mon, it made more sense to put it at the beginning of the dex rather than the tail end.
Why they never used the number 0 again? Well, they never released a mythical at the release of a new gen, expecting it to be used in-game. XY's mythicals were saved for later and SM had Magearna at release, but you couldn't get it until you beat the game.
