Actually this is the best way to handle M. Alakazam. Since all EX Pokemon 'evolutions' have been basic Pokemon they can make Alakazam EX without any worry over 'Kadabra controversy' then move onto M. Alakazam EX. By that logic Dragon won't be coming anytime soon either since we got M. Charizard EX. That logic doesn't make sense though since most people think we're not far from OS/AR being our next card set and the most likely candidates for the first round M. Pokemon are all of those types (M. Sceptile being Grass/Dragon, M. Blaziken being Fire/Fighting and M. Swampert being Water/Fighting, all of which have been done). Let's also remember that until we know the other M. Pokemon to appear in Phantom Gate, we can't even be sure the current trend will stay around regardless of OR/AS status.
But Nintendo is more than capable of breaking that trend regardless. I don't agree that they won't cover all of the Mega Pokemon and we could all debate our reasonings for against it, but in the end all we can do is wait and see because only Nintendo knows for sure, if anyone does at all.
For what it's worth, I suspect the Charizard we get will be the Stoke one, the one that was our FA Charizard EX in Flashfire. My next guess would be the Combustion Blast. With soon to be three different ways to get Mega Ascension Charizard EX (the box itself, along with the Mega Charizard boxes coming out soon), I doubt this is the one we'll get in the tins. I think in someways it's too bad that those boxes aren't coming with alternate artwork of M. Charizard X or M. Charizard Y, but I understand that to do so would probably be a bad move for Nintendo.