Some of them will simply disappear or others will be replaced by normal evolutions.

Think about it, we have already 48 Mega evolutions with ORAS and we will probably some more with Pokemon Z / X2 /XY or whatever. That's already way too much since you can only have one mega per battle (or having two in the same team on a VGC format). Even Gamefreak know that more mega will be useless since it would create way too much competition for a mega slot. And we also know that mega are designed especially for competitive battle (there are like 5 fives trainers with a mega in the whole game) so cutting or making less megas will be mandatory.

This is just some theory but what about proof ? Well look at how we evolve Mega... By using items and can you transfer your items in the 7th generation ? Probably not, pokemon storage and transfer revolves now around Pokebank and Pokebank cannot transfer items even in the same generations. So Gamefreak is free to put any stones they want or doesn't want from in the 7th generations. Also think about the +50 stones you must recollect AGAIN, at a certain extent the game will be way too crowded by mega stones...

It's still gamefreak so we could have no normal evolutions anymore and every pokemon getting a mega evolution but I really doubt it...