A couple of ways.
- Spam pilums and watch AI die of a heart attack.
- Spam fighters (not bombers, they are going to miss a bunch).
- Spam beams, especially the High Intensity Laser.
- Get a bunch of capitals with Hardened Subsystems, then outwait the phase ships.
Hardened subsystems is hardly necessary. A Doom only has the PPT of an Destroyer (low tech), and it runs out of CR faster once the PPT ends. That's before you consider that it spends the majority of the time phase cloaked, meaning that time runs 3-4x as fast for the Doom as your ships, so it's 420 second PPT runs out in around 150 seconds of combat. A Doom will actually run out of CR faster than a Tempest
without Hardened Subsystems.
Anything less than a Doom obviously runs out faster. More importantly, anything less than a Doom doesn't really pose much of a threat. AI is so *** when it comes to phase ships that you can pretty much just ignore them and nothing will happen, then they run out of CR and die, no problem.
If you are fighting at a much smaller scale and want to kill Gremlins and Shades fast without waiting 2-3 minutes for them to run out of CR naturally, the best thing to do is sit on them while they are in phase and just wait until they have no choice but to surface in your line of fire. Hyperion works best for that, especially with alternating phase lance (1 phase lance forces them into phase, the second provides a threat to keep them there until they run out of flux, then you pounce with both).