I have no problem with the effects of eng captain powers (although MW on a cruiser is rather laughable but I've been calling for percentage based heals for a while now and even explained it somewhere if anyone cares enough to find it, I think its in the "OMG nerf tacs" thread) and science needs a complete denerfing (starting by removing the movement debuff immunity from AP:O, otherwise that skill is fine and as stated a few posts back making AP:A and GDF only effective on weapon damage output) it will also however (as stated by cmdrskyfaller) a large change in the boosts given by skills in the captain skill table.

I think engineering need a wider range of boff skills as any more than 2 ensign engineers is a little too much to work with and all the high level eng boff skills (minus Aux2SIF3) are very situational in their effectiveness. But at the end of the day a lot of being effective does come from learning to play, a task I recently completed and now have 3 pretty effective builds (just need to tweak the tac/scort for maximum effectiveness and play with the sci a little and see if I can put together a more effective build there)