*scratches head* Vilegar is the only thing that has better than 50-50 to 'dos? Um...Magnezone? It completely annihilates Gyarados with any of its main points of attack. A good portion of the time, Magnezone will start with a Spiritomb, instantly purging them of their main trainer avenues: Poke-Turn, Junk Arm, Expert Belt, SSU, etc. Regi-Move my Spiritomb away? Sorry, I used a Collector for another 'tomb and two Magnemites and have already started evolving towards Magnezone SF or Magnezone Prime. Once SF is set up, it's hitting hard with a switch attack, bringing Spiritomb active and thus the lock begins again. Not to mention that once Prime is set up, you're using Judge as a great source of hand refresh, disrupting your opponent all the while. Let's also not forget that all it needs to do is blow two benched energies with a belt to KO a Gyarados, which most 'dos players will have a belt on as well, so that's two prizes.
The thing about Gyarados is that it's a solid attacker most of the game, but against a lot of the higher HP targets like Magnezone, it can't get the OHKO, especially when you consider the SF's ability to hit and run like the Cursegar of old. To contrast, 'zone Prime has limitless potential for a KO depending on the version you're running (straight Magnezone or MagneGatr) Also, Magnezone X's Electric Trans is completely absurd if you combine it with Seeker. Setting up your Tank that's loaded with Special Metals in one turn makes it completely irrational for Gyarados to even hope to take out when it's dealing with Trainer Lock as well.
The only way Gyarados has any chance at beating Magnezone is getting a better start (which is possible if all the pieces are in the right place, like using Portrait on a Collector or the 'zone player whiffing on starting with his dozen options for getting out Spiritomb, Collector and Call being main outs). If Magnezone even sets up 'zone SF, Gyarados is going to be scrambling to Seeker every turn to heal. If Spiritomb is KO'd, thanks, I use Twins to get another 'Tomb and something like the Level X or Special Metal if the X is already up.
In order for Gyarados to have a decent matchup against Magnezone (which will definitely see more widespread play as the season rolls on, especially if Gyarados remains popular) it's going to need to tech in Donphan again, or possibly use Seeker abuse with Mesprit in order to stop abuse of Electric Trans and Magnetic Draw. Even Donphan isn't foolproof because very few times does Magnezone SF ever leave itself open, and it can always Level Up to nullify 'phan's resistance. With a Belt, it'll still 2HKO a non-belted 'dos, and they wouldn't risk leaving 'dos belted anyway with the risk of being absolutely thrashed by the Prime.
Magnezone's options are incredible, and I'm surprised that more people aren't taking advantage of it. Give it time.