I just don't like the idea of megas. I have a couple reasons.
A. Some pokemon with megas were already pretty popular. Lucario, Gyarados, Blaziken, the classic starters (freakin Charizard got two). Aren't you glad your everyones favorite pokemon just got better? Lets also lump in pokemon already fairly strong, Tyranitar, Gengar, Alakazam, Mewtwo (why him? and 2 more?) and most of those in the already popular list. Butterfree still sucks in an age where Absol is fun to use. Lapras is an HM slave compared to Aerodactyl now. Oh Sableye is getting a mega soon? Did you forget about Kriketune, Vileplume and Raticate?
B. Some of the pokemon just needed an evolution. Aggron is in his final stage but still isn't all that great, OK lets give him a stone and he's a lot better. What about Bannette, he can still have an evolution. Houndoom has one more evolution left, too bad it gets a mega stone ending its line there. Mawile, you didn't even try to expand its line. No baby form, no trade item, no secret move, they probably would have used the same design anyways.
C. Some megas either make the pokemon ridiculously powerful or don't do enough. I'm going to have to go into competative play because the in game trainers don't know how to play against you either way. Kangaskhan isn't doing too well and is in the low tiers, lets give it a mega stone giving it a unique ability aaand it's in ubers, no one can use it now... Well how about Banette, it could use a boost, too bad it's still very low. Mawile on its own just sucks so if we give it a boost OU STAPLE, +12%usage, banned from all other tiers, that was quite a leap. This leads into my next problem...
D. Just how the stones are treated in competitive play. A lot of megas are used entirely over their non-mega forms. After all what are the downsides? You can only mega one pokemon per team, only a couple pokemon have stones (much less if you consider which ones are viable in your tier), and you have to actually find that pokemon and raise it then give it the stone. No one uses regular Venasaur but his mega is on 98% of them, guess we have to ban all of Venusaur from UU. It's not Venusaur that's broken, it's that one item and the new pokemon it makes only with Venusaur. The only way to keep a pokemon in a lower tier is if its megastone is banned in OU (Blaziken, Kangaskhan, Gengar) or it doesn't qualify for that tier and is BL (Heracross, Alakazam). I feel mega stones make a pokemon into something completely different: more stats, a new ability, 75% of the time it is an improvement, but then you can't use the non mega version.
Sorry I'm using competitive play as an example but thats partly why I don't like the idea of megas: they're given to already good pokemon, some could have still evolved normally, some do nothing or completely change the pokemon, and smogon feels it needs to ban certain pokemon based on one way (the only way now) of using a pokemon. I'd hope they don't get in the next generation but after all the work put into them and the Hoenn remake I think they're going to stay.