I think an interesting way to help fix the merc/commando issue would be to change around the eliminator pvp set bonus, and make them worth something. This why there would be no effect on PVE play due to ability changes, and the set bonus could be used to address the PVP problems.
Have the 2 piece add an effective root to a ranged attack. Then have the 4 piece lower the cooldown of the shield to 60 seconds and make it so you are immune to all controlling effects when in use.
do not touch my set bonus plox