I constantly see people complaining about how because of Blizzard trying to balance things around Arena's and PvP, certain specs get nerfed to hell and have damage and mechanics changed so that they're no longer (as) viable in PvE. So, why not use an idea that another MMO, with probably the best PvP I've ever played, Guild Wars used.
Essentially, certain abilities would have their values or functions changed once the player got into a PvP environment (GvG, Random Arenas, Alliance Battles, Hall of Heroes, etc).
For example: A Ranger (hunter) ability called Penetrating Attack in a PvE environment would do 5...21...25 damage (depending on your number of attributes in Marksman) and ignore 10% armor. However once you went into a PvP environment the values would changed to 3...9...10, still ignoring 10% armor.
Another example would be a Build or Spec that was Ranger/ Ritualist (Guild Wars allows for class combinations) where a Ranger would use an ability called Splinter Weapon (acts similar to Flametongue Weapon, Windfury Weapon, in the sense that its a temporary weapon enchant) which deals up to 50 damage to 3 adjacent foes and would last for 5 attacks, in a PvE environment, in a PvP environment, the damage would be reduced to 30. This weapon enchant would be coupled with a Ranger skill called Barrage, which hit 6 adjacent foes for up to +20 damage (works like multi shot does now).
The above would basically decimate people in large scale Alliance Battles (Battle Grounds the size of AV) and Guild vs. Guild fight because you're actually hitting each person about 7 times for upwards of 80-100 damage (before armor reductions), and given that health pools in guild wars capped out a 480 unaltered (no Runes or Glyphs of fortitude), you basically just one-shot an entire group of people.
There are other examples like Perma-Sins, IW Mesmers, IWAY Warriors/ Mesmers, 55 Monks, Riposte Warriors (my personal favorite), but the Ranger example was the one I had most experience.
TL
R, I suggest that Blizzard changes how abilities function when players are in PvP environments, as opposed to Nerfing the class's PvE viability.
Added suggestion, for PvP realms, have the abilities altered for PvP anywhere that's not a Dungeon or Raid.