Mega Alakazam:
- Ridiculously high Special Attack and Speed
- Amazing movepool with very wide coverage
- Susceptible to priority
- Terrible physical bulk
- Trace is extremely inconsistent
Mega Gengar
- Amazing Special Attack and Speed (not as high as zam's)
- Also amazing movepool with wide coverage and a myriad of useful status moves
- Typing grants immunities to Mach Punch and Extreme Speed
- Overall bulk isn't great
- Shadow. Tag.
Objectively speaking, Mega Gengar is better due to how horribly broken Shadow Tag is, especially when Gothitelle is slow and Wobbuffet lacks offensive presence. It can abuse things like Perish Song without a means of escape, it's nearly impossible to switch into it without a KO, and with any of its checks or counters gone, it can run rampant through teams without many ways to stop it. It's quite easy to see why it was quickbanned from OU on release and why it still remains in Ubers.
Don't get the wrong idea, though. Mega Alakazam is amazing.