EDIT: What about Dark pokemon? Are they allowed?
Do you mean Shadow Pokemon from Colosseum/XD? They've only been seen in Orre, and unless Team Snagem or Cipher interfere with the tournament, I don't think we'll see them. Oh wait. I think the greatest threat to the Pokemon world so far has been Cipher and their Shadow Pokemon (especially Shadow Lugia), maybe they can be involved in this thing! That would just be pure awesomeness!
Actually, I meant Dark pokemon like we see in the Team Rocket expansions (Like the TCG and what Shrimpy has on his site).
Dark pokemon, as per Team Rocket and Return of Team Rocket, are probably worse than Shadow Pokemon. Dark Pokemon are inherently cruel, a cruelness brought out with other methods than artificially closing the heart of a pokemon. It's not quite as reversible and the pokemon are often much more wild. They're meaner and harder to control, but they don't get any special moves like Shadow pokemon.
Imagine a showdown involving a trainer that totally loses control of a Dark or Shadow pokemon.