Ok it's gonna sound dumb but its the only way to say it- Us "engi's" need to be skitso [for lack of a better term] 1 set of skills for PvE & one for PvP, Seeing how our empathy doesn't seem to do much help [mines at 6 and doesn't seem to work] my PvP build is as follows-
Empathy-6, Suppression-3, Leech-2, Transference
Protection-3, Sheild Bubble-2, Sonic Boom, Pain(or)Decay-2
* Yes I use Suppression because it weakens if not dissolves the commandos crowd control & or singularity, It's been proven in PvP and by mistake on SY5, considering I'm told that their "pink cloud" attack isn't instant like our suppresion is it'll "kill" their charge

My PvE build is different in so many ways considering I don't use a lot of the skills as much as others but-
Leech-2, Empathy-6, Transference, Sonic Boom
Sheild Bubble-2, Decay-2, Protection-3, Revive-4

Every "engi" is different, we all have our different set ups and skill rankings but I'm sure we can all agree "Commando's may have the best armor but only WE can revive"