I really don't like Gyara's Mega evo for a lot of reasons.
Compared to Water/Flying, Water/Dark is honestly a bad defensive typing despite having 6 resistances. Instead of being weak to Electric and Rock you are weak to Electric, Fighting, Bug, and Grass, and Fairy (two of which Gyarados resists), don't have an immunity to Ground, have an even more unreliable STAB (lol bite what a joke), and the only resistances you get to condensate for it are Psychic (which usually have something like Focus Blast), Ghost (Gengar also carries Focus Blast), and Dark (rare outside of Tyranitar tbh)
Mold Breaker also isn't really that useful because SubDD already sets up all over Gastrodon and nothing else is really immune to water. It maybe helps against Rotom-W if you carry Earthquake but that's honestly the extent of it. Also, RestTalk is pretty bad since so much can honestly wear it down due to the myriad of weaknesses, its definitely not its best set this generation.
I still think Gyarados is good but its Mega-Evo is underwhelming.
Doesn't Gyara get Crunch? Damn, that's a shame.
About its new weaknesses / resistances:
The only Bugs that ever really see the light of day in OU are
Scizor and
Heracross, who are ruined by Intimidate and outsped by Gyarados anyway (not to mention normal Gyara resists all their STABs so it can stay in on them instead of immediately Mega-Evolving),
Volcarona, who can't risk a Waterfall, and
Galvantula (thanks to the new Sticky Web mainly) who already scares Gyarados BEFORE it Mega Evos.
As for its Ghost resistance and Fighting weakness... well, in both cases the most notable danger is
Aegislash (Shadow Sneak and Sacred Sword). Gyara switches in and weakens it with Intimidate. It can then see up Dragon Dance while remaining resistant to Sacred Sword, then mega-evolve before a boosted Shadow Sneak can even hurt it and annihilate it with Earthquake. If Aegis tries to Sacred Sword on the same turn Gyara attacks, it will be outsped and KOed anyway.
Gengar, however, it an issue, but Gengar is very physically frail and is outsped by a +1 Gyarados. It also has to choose whether to Shadow Ball or Focus Blast, based on whether the opponent thinks Gyara will Mega Evo or not - if it doesn't, it resists Focus Blast and KOed back with Waterfall anyway. Mega Gengar with its increased speed is of course still a threat, but quite frankly it seems quite obvious it won't be allowed in OU for much longer.
The psychic immunity is mostly useless, however it can allow Gyarados to check
Reuniclus better as its increased special bulk allows it to take Focus Blasts easier. Between its newfound special bulk and immunity to Psyshock, it can also halt
Latios and offensive
Latias fairly well as long as they aren't packing Thunderbolt.
The Dark resistance and loss of a Rock weakness, as well as increased bulk, make Mega Gyara a very good check to
Tyranitar. It can now switch in with ease on a predicted Crunch, and won't be punished nearly as heavily if it mis-predicts and gets smacked by Stone Edge. A Mega-Gyara's Waterfall will deal massive damage in return, too. Mega-Gyara also resists Sucker Punch so Pokemon like
Mega-Absol can no longer check it when it D-Dances up and starts sweeping. Also remember that it no longer takes massive damage from Stealth Rocks upon entry, giving it greater longevity if the user likes to switch a lot.
The new Fairy weakness is a bigger issue than the other ones, however, but most OU-relevant Fairies are specially bulky and specially offensive, with lower physical stats. With its great special bulk and the massive power (and flinch chance) of its STAB Waterfall, Mega-Gyara can effectively threaten most of them and, with some defensive investment, generally won't be OHKOed by Moonblast and the like. Especially after setting up a Dragon Dance, most fairies certainly won't want to take it on, with the exception of
Whimsicott who also resists both STABs and can annoy with Prankster Leech Seed, Stun Spore and Substitute.
Overall it is a mixed bag, but I believe a lot of positives arise from the type change. If only it got Crunch...