I don't think it can be stressed enough how important this review is. I'm gonna add in some more Pokémon, but I think dozens more could potentially be reviewed for brokenness.
Mega Empoleon possesses a phenomenal 84/118/141 bulk spread, something that not even Mega Venusaur can boast. With Bulletproof and only three weaknesses, it has potential to wall a large portion of the metagame. Newfound access to Roost and Defog in MFA give it a new niche, as well as make its base form more viable. However, granting it access to Roost did not make it particularly usable in the theorymon metagame some time ago, even in a meta filled with Fairy types. I don't think it's particularly bad, but it could stand some review (mostly due to its base 151 special attack). To fix this, I propose we don't go overboard with buffing its base form and remove Defog and transfer 20 base stat points from special attack to speed. Removing Roost would make it rather underwhelming.
I remember I mentioned underwhelming Pokemon with Bulletproof, and Empoleon was one of them. I hadn't realized it got Roost. O_O
The problem here is that Defog is a Gen 4 transfer move, and while it would (probably) lose compatibility with some attacks if we removed it from its level-up movepool, it would still make it usable and a big threat. Roost, on the other hand, can change the viability of its base form, and that's not the intention of this meta, right? And since I still think Bulletproof is a very situational and overall meh ability, I suggest
we remove Roost and give it Regenerator. I do realize there are already a lot of Regenerator megas, but it's the only way for it to gain reliable recovery without making its base form gain it as well. We also don't have to change the stat spread with this.
Mega Klinklang gains a wonderful ability to fit its base form's niche: Technician. Technician not only boosts its Shift Gear Grind to insane amounts of power off base 140 attack, but also renders HP Fire viable to round out its rather lacking movepool. Base 110 speed and the addition of the Electric type just make it worse for anyone trying to stomach Mega Klinklang's attacks. I propose we change Technician to Volt Absorb.
While I do agree that Technician makes it overpowered (Gear Grind roughly twice as strong as MegaKangas's Fake Out, plus access to Shift Gear), Volt Absorb would make it a rather underpowered Mega. Gaining an immunity to a type it resists is meh. I suggest either
Capacitance (One of the already created abilities, when user uses a contact move, the opponent has a 30% chance of becoming paralyzed) or
Iron Barbs. The former would clearly still make it a solid threat in OU, but it wouldn't be as overpowered as Technician. The latter would be a nice, balanced gimmick for setting up (it has 60/125/105 bulk), and it would make more sense than Technician, Volt Absorb and Capacitance.
Mega Stunfisk is another example of a super bulky 'mon with which I believe we went overboard trying to compensate for the sheer power in this meta. 109/114/129 bulk is excellent even by Uber standards, especially when backed up with (newfound) reliable recovery, two immunities (Storm Drain!) and only two weaknesses (Ice and Ground). I guess it doesn't have much of a niche outside of status spreading with Discharge and Scald, but it's worth considering. Physically bulky Mega Stunfisk walls quite a few top-tier threats such as Azumarill, Keldeo, and Bisharp. Again, this could very well be perfectly balanced, but I still propose we change Storm Drain to Static.
Stunfisk can barely status spread as it is. It indeed is a very good wall with a good ability and typing, but it can't do much. Giving it a status spread on contact ability would make it even worse than it appears, because the trainer might not even be able to choose burning or paralyzing the opponent. I propose we
change Storm Drain to Serene Grace and transfer 10 base stat points from both defense and special defense (20 in total) to attack. With this, Stunfisk's niche is boosted, it regains an weakness and becomes less bulky.