Steelix is already reliably countered by Vaporeon due to it not taking super effective damage from Earthquake unlike Entei. Sure Moltres resists ground but that's one move which is suboptimal anyway, so Moltres is only a marginally better counter than Vaporeon, not worth dropping Steelix down a tier.
Like no ones going to max out Moltres purely for Steelixes, they aren't that common and when you do see one, Vaporeon does the job. If it's still ranked as A despite it being countered by the one of the most ubiquitous Pokemon in the game, then it's probably going to stay there.
Raikou and Zapdos are quite big upgrades over Jolteon, so I agree with Gyarados being lowered. For Vaporeon it's not so clear cut since grass has the advantage of resisting water, you've got different type counters whereas Gyarados has one type that is clearly better than any other type (electric).
Although to be honest I'm not too fussed what happens, I don't really pay attention to the lists, gyms are hardly a challenge for any experienced player now.
