Gliscor and Hippowdon both have instant, reliable recovery, so that's less of a reason to use Vaporeon. Infernape, and Metagross and co. could benefit from Wish though, and Vaporeon can last longer than offensive Suicune through Wish + Protect, better checking some offensive threats. Vaporeon also has an immunity to Water, as opposed to a resistance. Suicune's better offensively, though.
Three Scarfers is still kinda redundant, so switching Flygon out won't hurt too much, except that it's arguably the most reliable revenge killer amongst your Scarf users. Magnezone can do better against steels, but Infernape and Flygon do well against steels anyway.
I'd switch either Metagross or Magnezone, probably the latter. Also, it's been mentioned, but switch Metagross to a more sweeping variant, or another Pokemon.
Metagross @ Life Orb/Lum Berry
Jolly 60 HP / 252 Atk / 196 Spe
-Agility
-Meteor Mash
-Earthquake
-Thunder Punch
Jolly to outspeed Scarf Flygon, Agility obviously to setup, Meteor Mash and Earthquake for general coverage, and Thunder Punch for [bulky] waters that can give your team problems, though you could also use Explosion to blow up in their faces. Fire and Ground are Metagross's only weaknesses, and most non-boosted neutral attacks shouldn't KO. When you expect an ground attack, usually Earthquake, you can switch to Gliscor or Flygon, and Fire attacks can go to Vaporeon/Suicune.
Another option you could use is the famed Sword Dance Lucario.
Lucario @ Life Orb
Adamant 252 Atk / 4 SpD / 252 Spe
-Swords Dance
-Close Combat
-ExtremeSpeed
-Crunch/Bullet Punch
Luke sports an immunity to the Sandstorm your team is focused around thanks to its steel typing. SD, CC, and ES are all pretty much standard. Crunch handles Celebi and non-Timid Rotom-A, though you may want to consider Bullet Punch since you don't have a particularly reliable way of KOing Gengar. Adamant for more power, but you can use Jolly to beat stuff like Timid Suicune or Timid Rotom-A.
You've got some decent checks for most flying types that could be an issue. If you can manage to fit Stone Edge somewhere on your team, then they're covered even better (maybe on Flygon, but Thunder Punch works better for many, since it's more accurate). Ghosts can be handled to an extent, though most aren't reliably KO'd (mostly since you don't have Pursuit to trap them, but they can still be dealt with). Suicune can beat most Physical walls, and Vaporeon can threaten them somewhat, though ones that carry Taunt can be a problem. Faster priority users such as Infernape can also be an issue, but Hippowdon does well against Infernape, and you can speed tie non-max speed ones, and Flygon can revenge non-Scarfed ones.
Whichever you go with, Stealth Rock
will help, since it can net them some KOs, and it makes it harder for Flying types to switch in frequently.
Hope I helped,
~FlameSaber