It's a little more complicated than that unfortunately...When Zubat evolves into Golbat, Golbat has the ability to add 2 damage counters. To be the same as Bats, and every other "When this Pokemon evolves etc..." ability, it would have to be on M Alakazam EX, not Alakazam EX. Once you place M Alakazam EX onto Alakazam EX and evolve it, it overwrites all traits on the original Alakazam EX. Therefore, it would no longer have the ability to activate.
It would need to say something like "Reveal M Alakazam EX from your hand. If you do, place 2 damage counters on the defending Pokemon and 3 damage counters on up to 1 of your opponent's benched Pokemon, then place M Alakazam EX onto Alakazam EX. This counts as evolving Alakazam EX. You cannot use this ability on your first turn or during the turn you play Alakazam EX." Just as an example. It would have to have some way to evolve into M Alakazam EX other than the standard evolution rule.
Actually, this is incorrect.
The text on Golbat is as follows:
"When you play this Pokémon from your hand to evolve 1 of your Pokémon, you may put 2 damage counters on 1 of your opponent's Pokémon."
The effect triggers when Golbat is placed from your hand to evolve (obviously on to Zubat). Now, with Alakazam EX, the ability of that Pokemon activates as a result of the Evolution, not the action of the Evolution, which is how they will justify why it will work. Basically, because of the following:
A. Evolving in to M Alakazam EX does NOT change the actual state of the Pokemon itself (I.E. when you AZ a Pokemon like Crobat, for example, you add all the Pokemon below it because they are not attached technically, if that makes sense. Basically, even though Alakazam EX is in its Mega Evolution Form, it is still the Pokemon Alakazam.)
B. Because of A, the trigger of the ability will still activate, regardless of the new form of Alakazam.
Also... it's a specific rule stated on the card that requires a condition of Evolution... which probably will be the actual justification they use if they need to use a justification, making everything I just said above a waste of 3ish minutes.
Huh. :l
Still, TL;DR: They may have made this much more complex than it needs to be. Still, it'll work because they designed and printed it. #PokeLogic