I think Gyarados is pretty bad this generation... but anyways. Assuming this is turn 2, my opponent explodes o- err... explosion sucks now so... my opponent destiny bonds me while I have a really bad lead I guess... Whatever. Vaporeon is generally known to beat Gyarados. First, I assume either boiling water or toxic. If it's Wish or Protect, they wasted a turn, personally. Actually, since my opponent knows my team, they may try to use other offensive moves... I don't really fear HP electric, I feel it makes Vaporeon really weak. Ice Beam is alright, but it doesn't KO the new dragons, so.... Vaporeon sucks lol. I don't even know why the hell I would bring out a sweeper like Gyarados on the second freaking turn. He's not mixmence.
Deoxys-A doesn't Levitate so there's no point in Stone Edging. Scarftom is faster than a DD'd gyara. Gliscor would never come in on Gyara unless it carries Stone Edge. They don't. Deoxys doesn't really enjoy coming in because the risk is too great. It would be a waste if your opponent's bad moves lead to your loss. Gyarados needs like 4 hits to kill Vappy while Vappy needs like... 20 if it uses Boiling Water without getting a burn. Ice Beam takes 6 at best. HP elec kills in 2, but I would assume the set Boil Over, Toxic, Wish, Protect since it performs the best imo. Different experiences lead to different decisions... Rotom could come in on Earthquake and force me out, but a good Vaporeon already does that. No need to waste a turn to beat something you already beat.
I would definitely bring in a status absorber or steel vs the vaporeon. Ideally Roopushin or however you spell it. Guts through status and kills everything short of Gliscor. Rotom could tbolt me once status wears enough of my hp away... or immediately if he would rather have another one of his Pokemon live. Vaporeon combined with toxic orb Gliscor sounds pretty potent, actually. Balloon Doryuuzu would have to come in and dance in its face then.