It's slow.
Obviously you won't be using MGyara as a revenge killer except for the absolute slowest of mons you know you can beat. But it's base 81 speed is quite slow for a DDancer, one of the main reasons Dnite no longer dances anymore. While its newfound bulk is quite (read: very) good (95/109/130), you have to mega evolve to take advantage of it. Water/Dark isn't bad defensively, but its quite easy to take advantage of with the plethora of mons with fast U-Turns/Volt Switches and powerful, fast fighting types everywhere (namely, Keldeo). Not to mention the Lati twins who can easily decimate MGyara with a Draco Meteor.
Gyarados easily makes up for speed with great power and great typing(And intimidate in base form) before and after mega evolving. It is pretty bulky, so the VoltTurns won't OHKO it and it can easily DD on those. And M-Gyarados is a pretty good Lati@s check for a reason..
252 SpA Life Orb Latios Draco Meteor vs. 0 HP / 0 SpD Mega Gyarados: 220-261 (66.4 - 78.8%) -- guaranteed 2HKO <- Wouldn't call that easily decimate.
Point #2:
It has 4MSS
This is an argument thrown around pretty often in why certain mons are checkable, should be banned, should rise/drop, etc. But MGyara truly has a serious case of 4MSS. As a DDancer, it would love to run DDance, Taunt, and Dual STABs ideally. But to get past mons like Chesnaught, Breloom and MAltaria, it would love Ice Fang. But in order to ensure certain KOs at +1 as well as not being walled by Keldeo and Azumarill, EQ would be nice. But because priority and fast megas exist, Sub would be awesome to prevent being revenge killed. As you can see, and already know, MGyara can't run all these moves. It can only run 4 and pick a mon to be walled by.
M-Gyarados easily makes up for this with raw power with only its STABs, unblockable taunts(mental herb lol), and superb bulk. And you seem to grossly understimate Gyarados' bulk, no form of priority can take it out in one hit. Scizor's Bullet Punch does nothing, so does Azumarill's Aqua Jet(though you should only be switching in when in base form), Talonflame can't OHKO, M-Pinsir can't OHKO with Quick Attack, even at +2, M-Lopunny's Fake Out = 0, need I go on? And it doesn't really need Sub because at +1, I believe you outspeed M-Beedrill if Jolly. Really, DD+3 Attacks is amazing, and Sub+Taunt+DD is also decent. I am sure a ton of Pokemon would like to run 6-8 moves, even S Rank Pokemon, but they define the meta, so I doubt they'll be dropping for that.
Point #3:
Weak STABS
I wanted to phrase this as MGyara being weak, but the real issue is the relatively low base power of his STABS. With Waterfall and Crunch being only base 80, MGyara has to rely on getting to at least +2 in order to effectively sweep.
Getting to +2 with Gyarados isn't too hard, thanks to Intimdate base form and excellent bulk and Sub. And off of Gyarado's horrifying 155 Atk stat, those base 80 power moves still hit super hard even unboosted.
Point #4:
It requires extensive support
MGyara is weak to SR before Mega Evolving which puts pressure on how many times it can switch in due its lack of recovery. Not only that but it is often used as check to physical attackers with access to Intimidate which requires it to take additional damage further ruining its chances of potentially tanking a much needed hit to continue to sweep. MGyara doesnt like directly switching into mons like Heatran or Ferrothorn directly for risk of a burn or being seeded or even a stray paralysis. In other words, it's quite easy to force out and keep out to the point where its not even used at all. It's similar to MSharpedo in that its best kept behind until lategame but that's essentially playing with a forced handicap in order to ensure that it can even set up. (hence, the extensive support). Not to mention that its weakness hurt it far more than its resistances help it.
Almost every teams needs hazard control, so that point is invalid. And Gyarados forces so many switches, so it won't being taking too much damage. Heatran often sets up rocks or goes for Lava Plume, so in 70% cases, Gyarados gets a free switch, and a water type that can't switch into Ferrothorn? How is that anything new? No one is using Mega Gyarados as a revenge killer, it sweeps late game or sets up early for a sweep. Again, you must be either using Gyarados wrong or not using it at all. Intimidate base form, excellent bulk before and after mega evolving, and how does its typing hinder to more? It checks the Lati@s, Megagross, Bisharp, Mega Scizor, and Zard-X THANKS to its typing. I wouldn't call that bad.
So, M-Gyarados should stay A+, for its great bulk, nice typing, and excellent power.
Edit: Ninja'd.