Sounds like an awesome change. I think perhaps the changes you are making to support it could be used in other ways? Maybe an 'Entropy Cannon' that slows down time for a ship hit with the shells?
Oddly enough, the fast-time shenanigans came along before the phase changes for another reason, and then just seemed like a good fit for phase cloaking.
I experimented a bit with adding a large speed/maneuverability boost to the phase cloak system (combined with reduced combat deployment and increased flux costs) and it seemed to work quite well even with the current AI (although it still had a number of Phase Cloak AI pitfalls). It seemed to work best with strike weapons and with ship systems that were also strike-ish (i.e. increased RoF for a brief time).
Yeah, strike weapons definitely feel most useful - or, at least, weapons that can get most of their damage out during the cloak cooldown. Although something longer-ranged can work pretty well, too.
So, yeah. Even if burst damage doesn't outright destroy a phase ship, it would cripple it anyway.
I wouldn't count on being able to nail them with burst damage, really. The impact of the cooldown is mainly in phase ships needing to be more careful about where they unphase, but they *are* careful. You can defend by moving your shields and weapons to track the ship, but it's not going to uncloak in front of your AM blaster/etc if it can at all help it.
If the new mechanic prove too powerful, what could be interesting is that EMP damage extend a bit (maybe one or two seconds) the time a phase ship need to be able to phase out again after uncloaking. It wouls add a nice incentive to mix your loadout.
Neat idea!
At the very least, ship can hide at the edge or corner to prevent ships from flanking.
I wouldn't count on being able to do that nearly as well (or at all) in the next release.