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I used to play my tier 2 then later my tier 3 as an electronics warfare ship. They are fairly viable to endgame, but unless you take a very select set of skills, you will have problems with STF missions. My carrier, and nebula before it, uses the healer idea, along with a fair amount of shield stripping to be viable. The thing is though with the nebula (and other science vessels), although you are perfectly viable at end game, you will feel somewhat lacking. Escorts will out damage you and cruisers rarely need any aid, unless your on an Elite STF, and for some reason, you will tend to draw almost as much NPC attention as the escorts.
But seriously Science ships are Great IF your captain is a science type
And you have Good (Read Vulcan) officers
I've actually found an Eng Captain to be a good fit on a Sci vessel too. Rotate Shield Frequencies plus Miracle Worker won't make you a tank but it does dramatically increase you survivability, especially if you kit your ship out to have really good shield performance. I built myself around power drain, especially focused on taking shields down for quick, brief periods. My alpha strike is generally popping EPS Transfer as I approach, holding fire until I can fire a Tyken's Rift and then immediately following up with Target Shields. Then I pop High Yield Torpedo and wait for my chance to strike their hull in the window of opportunity while the shields are down. Many times I'll follow up with Energy Siphon and Fire at Will, which keeps shields weak (and sometimes drops them a second time) and lays down somewhat improved DPS as I ride EPS Transfer out.
I haven't found my build very efficient in PvP, but I don't PvP all that often and I generally don't enjoy it anyway. I squared off with a friend of mine flying Tac/Tac and could generally only manage to slow him down, keep him on the defensive and disrupt his ability to alpha strike me while I had a hard time making a big enough dent fast enough to prevail. When I've played regular matches, I tend to be an aggro magnet for some reason I haven't been able to fathom (like I said, my build doesn't seem overly effective in PvP), and when I end up with 3 to 5 people ganging up on me I can't really last long.
I do decently well in STFs but the two core problems I've encountered is A) I can't bring much straight-up DPS to the table and B) people who fly cruisers don't seem to actually do much tanking in the "draw aggro" sense. My build would be really effective if I have an Escort as a backup, who waits for me to slow enemies and strip their shields. In Khitomer Accord Space, I'm great at slowing down the waves that head for the portal but I just don't have the DPS (at least at Elite) to destroy those ships fast enough.
So yeah. To summarize, Eng Captain on a Sci Ship is modestly effective, and more to the point, very fun. Cutting a cube's shields and then knocking enough health off to be measured in increments of 10% in the first fifteen seconds of combat? Priceless.
I love the science ships! They are so... goofy spacey in their designs. I find they work just as promised: Mild DPS, mild tanking, heavy debuffing and shield stripping. (The downside is that at Admiral ranks a lot of the bosses simply shrug your attacks off anyway and so the fights are looooooong.)
Also: I've found ground combat, with all of the debuffs and area effect attacks at your disposal, to be ROFLstomplicious. Even more so than using a Tac or an Engineering team with oodles of turrets.