Top 3 least viable PvP specs:
1) Arsenal Mercenary
2) Lethality Operative/Sniper
3) Annihilation Marauder
The reason is very simple, and everyone already knows the answer. Sustained damage, and especially DoT damage, are inferior to front-loaded burst damage. Annihilation is perfectly fine for the Marauder who likes to PUG and needs additional survivability or for anyone just running normal PvP. RWZ are all about focus fire and burning through targets quickly. The burst of Rage or Carnage are much more desirable, and Carnage also has roots and improved Predation that are more of a benefit to the team than small group heals.
Annihilation is fine as-is. It performs very well in all aspects of the game, except RWZ, and there's no need to tweak it.
I agree with everything until the last paragraph. You think it's ok that a spec is unviable in competitive PvP? Saying "this is the pug skill tree and this is the RWZ skill tree" is pretty lame don't you think?