As a predominate Commando/Merc player (Commando Heals and Merc Arsenal), I'ne noticed quite a few things.
In regards to Arsenal, the problem seems to be mobility. All of the main abilities are casts which are a root on myself in of itself. I understand that when played hugging a wall, a Merc can put out a lot of DPS, but it's so rare that we are in that situation...Once a Mara/Sent leaps, interrupts, and roots us, it's game over...sure we can prolong the inevitable but it's a tough task asking to beat them out 1v1.
Even for my Commando healer I have better survivability and mobility. Most of the time I'm focused by at least 2 players on the opposing team. I've got Bacta Infusion (can be used as an on-the-run heal), kolto bomb, and even the trauma probe serves as a damage mitigation. Tease them with a MP (will be interrupted) and then use AMP. Stay on the run, toss shield when in LOS of the ranged dps, rinse and repeat. Now Commando Healers have plenty of problems themselves (don't get me started about the hammer shot being a complete waste in PvP - "Hey everyone!! I'm over here! Come get the healer!") but with Merc Arsenal, there's no such mobility. Unload has a cast, Power shot has a cast, tracer missile has a cast, DfA is ineffective when playing a decent group, rocket punch doesn't even seem to root them anymore...the knockback version was better! I'm forced to stay in close against melee speced opponents! And even if I do get some distance from them, their Force Leap has just cooled off..
I don't usually comment on the forums (hence this being my first comment!) but i was getting really frustrated last night PvPing with that Merc because the other classes know that Arsenal is dependent on casts... I read a comment about Merc's being a Rooted Turret and couldn't agree more.