For years already we've have a balance struggle focalising on numbers, yet what's taken out for one side the game end up becoming a hole for the other side of the game. Unfortunately, PvE and PvP/WvW give players 2 vastly differents environment on which some profession's tool end up with imbalanced result.
What is the issue:
Closing the gap generated by the lack of boons in PvE:
This is a tricky issue, because adding more boons in the gamemode won't fix it. Ideally, mobs would start to rely on boons, have their stats nerfed, their AI improved, they would gain the ability to dodge... etc. This is an impossible task.
The only real possibility is to give mobs with the defiance/breakbar system a permanent stack of vigor (much like the boons that can be given to the training golem). That way, there is a permanent boon that could be exploited by the boon hate tools, without affecting outcome of the fight for professions that don't rely on boon hate.
Closing the gap generated by the lack of conditions in PvE:
Here, there is no real reason to see conditions so underused and misused in PvE. Why they are used in burst when the PvP scene already show how bad such design is for condition is a mystery.
The easiest way to fix this issue is to remove aoe power damage pressure from PvE boss encounters. Remove those unsightly power damage that aren't especially associated to boss move and replace them by poison stacks. If those damages come at an interval of once every 3 seconds, make it so instead, it apply 10 seconds of poison every 3 seconds. Other that that, just add weakness and/or cripple to some of the mobs attacks. This will make encounter more challenging and at the same time it will open room for condi hate tools, all while reducing the gap between PvE and PvP/WvW.
You'll be able to start seriously work on balancing numbers.