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Let's take a look.
>Typing gives weaknesses to a lot of unfortunate typings, including Flying and Ghost (both of which are much more common than before)
>Speed is good, but not fast enough to outspeed important threats
>While not frail, he's still pretty weak defensively
>Only priority is Fake Out (unreliable and easily abused) and Bullet Punch (which has very meh coverage and isn't STAB)
But in the end, many of these are problems that a good amount of Pokemon face, just with different weaknesses. Mega Medicham's main weakness is circumstance.
Is he powerful? Absolutely. However, despite his incredible power, he's very easily revenge killed by Talonflame and Aegislash. Mega Medicham's situation very much like Kyurem-B of Gen V - it's powerful, but if Scizor can switch in and KO with little effort, then you aren't as effective as you could be.
While it is true that Talonflame and Aegislash are only checks to Mega Medicham, they're big enough checks to take Mega Medicham out of the spotlight. The fact that it has to compete with other Megas such as Lucario, Gyarados, and Pinsir for the team selection also makes it very difficult for Medicham to stand out. Why pick Medicham as your Mega when other Megas are much better equipped to take on Gen VI OU?
In the end, Mega Medicham is good, but the fact that it's countered by some of the top threats in the game makes its life hell. Add in that it isn't easily fit into teams unlike other Megas means that users of Mega Medicham will have to build the team around it - and that's something that will always hurt a Pokemon's usage.
tl;dr: Mega Medicham's weakness to top threats like Aegislash and Talonflame makes him difficult to choose over other Mega Pokemon. This alone makes him tough to use.
