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I don't think Deoxys-D is overpowered. One thing for sure, he's annoying and trashes the early game.
Too powerful ? no.
Turns first steps of the game into shit ? yes.
Ultimately I believe it's just another threat in the metagame. If you are prepared for it, it will be about as troublesome as garchomp, ferrothorn, tyranitar, or any other guy.