I might be a little biased (XD), but I chose Deoxys. In-game it is probably the most versatile pokemon besides Arceus, and all of its forms can hold their own pretty well.
Also, in the movie, although it was defeated by Rayquaza at first, Deoxys seems to have more long-term energy that Rayquaza. Sure, it comes in these magnificent burst of power to stop Groudon/Kyogre or to blast at Deoxys, but Deoxys can keep going for a lot longer. Plus, Deoxys has regenerating powers, and can still live with only its brain-thing remaining.