The problem with M-Gyarados is you give up a lot of what made Gyarados good. Resistance to Grass, Fighting, and immunity to Ground. You Mega-evolve and suddenly that Mach Punch is a lot more threatening. Plus weakness to Fairy? Additionally, Gyarados has a huge variety of items it benefits from. Lum Berry, Sitrus Berry, Life Orb, Leftovers, Shell Bell... all gone if you want the Mega.
For comparison:
Gyarados:
Weaknesses: 2
Resistances: 5
Immunities: 1
M-Gyarados:
Weaknesses: 5
Resistances: 6
Immunities: 1
Not saying it doesn't have uses, and Mold Breaker is an undeniably good ability, but it requires a LOT more careful playing/scouting for threats.