The disregard has gotten so bad that many people take the PvP set bonus over the PvE bonus. For a mere 5 energy, which becomes useless once you dip below the top regen rates.
You're mixing up set bonuses.
The pvp FOURSET is +5 energy.
The pvp TWOSET is +15% healing on recuperative nanotech. This is the one people pick up. You can see why it works well with the pve 2-set I assume?
RN is in almost every fight going to heal more than your kolto infusion. Much more generally when used on cd.
Assuming 75% surge w/ accomplished doctor then a 15% crit rate for kolto inf is close to a 15% healing done on average. It's a little more than that but for simplicities sake we'll say it is.
Basically the pvp 2-set will provide more healing on average AND provides it statically rather than on a random chance.
As for cunning/overkill augs, the difference is so small no one who has looked into the maths gives a **** what you stack. That said in pure hps numbers cunning is going to win even at cunning levels in the 2500's. I don't even know why you brought those up but there you are.