You don't have to swap out your eng if he doesn't have one skill you want, you can just retrain them at sol.
I use torps front and rear; rather nice when someone gets past you on your side and starts to head to your rear so all you have to do is waggle your pointing a bit and launch a salvo of torps.
I haven't looked around about it much yet, but does everyone get the same base model of a class tier when they advance? If so can you just go to the customization place and have it swapped to another model of that tier?
A little weapon advice, phasers are good. I had noticed a couple times while playing that for some reason my shields would just drop. Apparently the secondary bonus ability of phasers is a 5% chance to disable a system, and if that system happens to be shields it causes them all to fall.
Also there was a math thread on the forum, it was mainly about lack of turn rate on cruisers, but it seems items which just have a small % add or subtract ability when compared to another item with a different ability isn't that good when considering how the games hard code formulas handle it.
When it get to the point where I have 4 forward weapon slots, think I will stick 2 of them with torps. While a torp use will cause a global cooldown on all torp launchers (let's say 6 seconds) it's still less than the cooldown to reuse an individual launcher.
For BO skills, I have my lt eng with shield polarity (real nice) and emergency power to eng, my other eng with emergency power to wep, tac with high yield, and science with jam sensors (a rather nice one when dealing with multiple contacts as you effectively remove one for over 10 seconds).