I have two, my JHAS which is unreal and massively OP LOL and my Mobius Destroyer with all the consoles including the Temporal warfare set.
Which is best? Well the JHAS is best for raw unadulterated killing power but because of this you'll seldom see me in Kerrat with it, it just seems unfair to use it on RA ships that have little to no chance.
So I would go with the Mobius as it is more fun with all the time travel stuff and flown by a sci it is awesomely destructive, almost up there with the Bug and in fact has seen off a few bugs to date.
If I went with non lockbox ships then I'd say Fleet patrol escort for tac, Oddy or Regent for Eng and the Nebula for Sci.