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At the start of all regions, the first PokéDex number is usually 001, being the Grass-type Starter. Why is Victini 000 in the Unova PokéDex?

Are you asking why Victini is the only Pokemon with #000, or why it has #000 in the first place? It wouldn't make much sense to have Pokemon share dex numbers so I'd assume the latter?
It's a gimmick. Makes sense considering BW uses an entirely new cast of Pokemon.
Well, through REGIONAL PokéDex, the only #000 would be Victini, counting all regional PokéDexes from Gen 1-7.

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Victini is a special Pokemon. It is obviously an important part of Unova (folklore and otherwise) as seen by its major appearance in the movies. It is, however, not a mascot Legendary, but maybe the creators thought it required its own unique way of commemoration, which was done through its novel Dex number. As is rightly pointed out, this is significant only in the Unova Dex, because it is #494 in the National Dex.

While we don't see it being mentioned much in-game, it obviously has a kind of kind of importance like Celebi or Jirachi (but to an arguably greater extent) outside of the games, in movies, where the folklore of Unova is more prominent in the story. Another thing might be its uniqueness as a Pokemon dedicated to be a good luck symbol or charm, its main use being a symbolic victory mascot over being a raw powerhouse that one can use in battle. This is reflected in its Dex entry which claims

"This Pokémon brings victory. It is said that Trainers with Victini always win, regardless of the type of encounter."

which is, practically speaking, impossible. So what we see is a more superstitious approach to its function, as opposed to a logical one. Again drawing on superstition, there might another couple of reasons, being, that

According to an IGN interview, Victini is Junichi Masuda's favorite Generation V Pokémon.

and another that the company officials probably thought it symbolic or good luck to have the Victory Pokemon at the very beginning, to ensure success of the Generation 5 games. This is probable due to the fact that Junichi Masuda is an important person for Pokemon, and his opinion carries a lot of weight, and also by the fact that company officials are human as well, meaning they can be irrational and superstitious at times too.

Source for Victini being Masuda's favourite Pokemon is from its Bulbapedia page.

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Thank you, ~Rex!