This thread fascinated me, as I roll with an engy in a science vessel. My two bars of latinum:
It's a bit tricky to solo in. Since you're not king of the dps, it can take you a while to finish people off. That said, with the high shields, you generally have the staying power to finish the job.
My engy is generally used for flying with my fleet and playing the healer role.
Since the science vessel gets the aux bonus, healing powers and anomaly powers (i.e. Gravity well) are excellent choices. Personally, I bork my weapons power and fly as a torpedo boat with two in the front and one in the back. I've been using the Breen transphasic so I don't have to worry so much about getting the enemies shields down.
I'm currently trying a turret build (one in the front with two torps, two in the back with one torp), and utilizing high yield torps and cannon rapid shot (turrets are cannons). Seems promising so far, especially in my support role.