Right now my feeling is it's only a tad overpriced - but it's hard to say just how much versatility is worth. Aside from changing individual ships, there's also the possibility of giving phase ships some special campaign-level mechanics.
Thant would be neat, would it be something like being able to chose were on not to engage an enemy fleet if all of you ships are phase or something more subtle...
I'd like them to not be visible on the fleet map. Like, when you mouse over and see what a fleet has.
Eg.
"The design of the Doom-class phase ship interferes with long-range sensor systems. Though quite visible to visible light and short-range radar, it remains nearly invisible to long range detection systems. This technology has proved to be quite invaluable in baiting patrols and pirate fleets into otherwise hopeless engagements. They only realize that a trap has been laid when they are too close to avoid engagement."
Which would provide incentive for a civilian level ship that detects phase ships and allows you to see them prior to engaging with the fleet. From a gameplay mechanic, it would keep you on your toes about engaging a small fleet without the proper detection ships, and it would let players have a way of clearing out those small, fast harassment patrols and fleets that are too scared of a normal sized fleet.
But, thats just my take on it!