I think one limitation to megas that many people overlook is that it will consume their item slot. The extra power of life orb, the extra survivability from leftovers, or even the surprise factor from sash/scarf will be greatly missed.
I believe that they'll slowly introduce megas; not all at once, but definitely more than the 7 currently revealed will be in XY. It's worth remembering that the work in each mega is essentially the same as designing a new pokemon. Expecting 700+ megas all at once is unrealistic.
This is what I'm expecting: XY will have 40-80 megas. The sequels/thirdversion will advertise itself as introducing a new 50 or so megastones. With every new generation, we can expect that they'll introduce less-and-less new pokemon, and make up for it by introducing new megas. (No, not completely stop introducing new pokemon, but it's easy to imagine Gamefreak only introducing 80 or so when we get past the 1000's.)
As a more extreme theory: I do not believe any Kalos pokemon will have megas until the sequels and beyond.
Keep in mind that Arceus's Multitype ability relies on it holding a plate. Yet Megas require holding a mega stone. I think this makes Arceus among the least likely to have a mega.
The only solution to this paradox I could imagine would be Mega Arceus holding a "supreme plate" as a megastone, in which he changes type right before performing a move. So if Arceus used Shadow Claw, it would change into a ghost type. And right before you can hit it with a ghost-type move, it'll use ExtremeSpeed, get its STAB back, and be immune to the upcoming hit.
