Interesting, I guess. Could have the counterpart to Deoxys be Jirachi, the other Space legendary, could be the soother if things go wrong for the protagonist.
I was going to pick mew or mewtwo, but the 1st movie is like that, and I didn't want it to seem like I copied the anime, but they still make an appearance at the end of the game along with a bunch of other Legendary Pokemon, and I already have planned out how they clone people.