Hm. For a competing viewpoint, I find them a bit of a nuisance, but not a serious threat. Then again, I tool around in a Gedune cruiser with maxed combat & tech skills, hardened & extended shields, etc., so, err, I don't find high end destroyers to be serious threats either.
I do agree that their phase cloak upkeep seems a bit low, but they make up for that by randomly de-phasing so I can kill them (CEPC turrets work well enough for me), so...
I'd think that increasing phase upkeep, flux capacity, & speed, along with giving them some flux-hungry weaponry (AM blaster, or IR Pulse Laser, or the like) might be good... but I'd like to see them move in, hit a target, move out to vent, and I'm not sure the AI is smart enough to do that. Worth some playing around, but the current state isn't bad.