Most player ships can and should go without PD, except token to cover engines from Salamanders, at least until capitals.
BurstPD is good at removing few high value missiles but is easy to overload or spoil with flares.
Without IPDAI any non flak PD is not to be relied on. With IPDAI I'd rather use IR pulse, at least on Conquest or Odyssey.
For AI ships I just put few cheap LRPD/PD lasers - that's as much as makes sense without IPDAI.
I don't typically use IR pulse since its flux is higher than typical PD equipment of similar size, and I know things can get out of hand fast when bombs and rockets are coming.
Meanwhile against mines, burst PD is very effective so long as they don't get flared, unless IPDAI is installed to deal with that on top of dealing extra damage to missiles and mines.
Defensive Systems 3 for phase ships is generally bad. With 4x speed, they burn through PPT faster and lose the endurance game faster against enemy phase ships. The only time it may be useful is Harbinger playership that desperately needs more speed to outmaneuver enemy ships like a phase frigate.
I definitely do not want Defensive Systems 3 on an officer assigned to a Doom.
As I personally use phase ships and let other officers use other ships for frontline combat, I use DS 3 to quicken my movement and weapon fire while phased, especially when I am armed with 2 antimatter salvo pairs, phase lance pair, and Typhoon launchers. I sacrificed PD for maximum flux capacity, and use resistant flux conduits to vent faster than increasing flux vent for the same points while resisting EMP weapons.
Harbingers are pretty effective phase killers due to its system ability to overload a ship. A brief enough time to use fast spike damage weapons before they cloak. It would have a harder time with a Doom since it has more flux capacity and the mines, but everything else is fine.