So... here's a crazy theory... Deoxy's is an Ultra beast, or from the same area/world as the other ultra beasts.
Deoxys' can change its form. Its not from this world, and it doesn't look like any sort of pokemon we have seen since, till the Ultra Beasts The way it moves and looks in the new generations short reminds me a lot of what we have seen in game for the ultra beasts
Just to throw this out there, but in X and Y, Mewtwo received
two Mega Evolutions, despite the fact that Mewtwo played no part whatsoever in any plot relating to the games. Kyogre, Groudon, Rayquaza, the Latis, and Diancie all had the some form of home generation advantage. The biggest part that Mewtwo has ever played to any plot in the games was some out of the way lines of text from Pokémon Mansion on Cinnabar Island, and what amounted to an end-game quest in the otherwise fairly basic games of RGBY. He didn't even get that much in HGSS, let alone XY.
Because of this, I wouldn't mind it too much if Deoxys turns out to be an Ultra Beast, in part because we don't even know what the Ultra Beasts are, and because we know that they're not above either retcons or significant interactions with non-significant legendaries. Of the legendaries of the first six generations, Deoxys is among those that seem to come closest to the Ultra Beasts, whatever they are.
So, this thought isn't something that really relates to what I was just talking about, but it came into my head, and I just had to ask it. Would it be worth it, if Mega Stones could act as Z-Crystals, if upon using the Z move, that Mega Evolution was lost for the battle? That is, if the pokémon has yet to mega evolve, it can no longer do so if it uses the move, and if the pokémon has mega evolved, then it reverts to its base form after the move, and again, it loses it's evolution capability. The more I consider it, the more broken it sounds, but it could be an interesting end-game nuclear mechanism. It would have to function as a species item, of course, so it wouldn't necessarily be turning a Mega Gardevoir's Hyper Voice into the Fairy Z-Move, for example. Just something that conceptually burns out the remaining energy that sustains the form. There are some interesting mechanics that could come from that alone, such as the power of the move growing weaker the more turns that the Mega has been out, for example.