It's been two in-game years and I still haven't seen a single Ion Pulser, either in a market or on an enemy ship. I finally resorted to consoling myself one just so I could test the thing. First impression is that the sound is terrible. The Ion Cannon makes a satisfyingly snappy noise, but the Ion Pulser makes a quiet little thwippy sound, like a piece of paper in a bike's wheel, which does not do the weapon's power justice. You need another weapon to deal some hard flux damage first, but once they hit 80% or so they might as well have overloaded because the Ion Pulser will make sure they're not gonna do anything for at least 15 seconds. It's worth the OP, if you've got the flux dissipation and the other weapons to back it up.
The new Doom is insane. It was a decent ship before, but it's an absolute monster now. It's got the peak time to really abuse the new phase mechanics, the new phase mechanics more than make up for the loss of Fast Missile Racks, and the new ship system is amazing in its own right. This thing eats cruisers alive and kills the simulator Paragon in a couple of passes. Don't even ask about what it does to Onslaughts, it's too graphic to describe on a SFW forum.
The new Aurora is disappointing. The only energy weapon you can realistically put in the small synergy hardpoints is the AM blaster, but the new phase ships are much better AM blaster platforms because they'll almost always have the speed and positioning advantage as well as not having to worry about risking an overload from soft flux. So either you're piloting a burst-and-run Aurora which is very inferior to a burst-and-run Doom, or you're trying to use the Aurora as the hybrid energy/missile boat it used to be but now isn't because it doesn't have a large missile slot anymore. You can't run anything similar to 4 Annihilators + Locust because the Annihilator Pod has no burst, the Harpoon Pod doesn't have enough sustain, the Typhoon doesn't fire fast enough, and 4 Swarmer SRM launchers are inferior in every way to 1 Locust SRM launcher. You're stuck with slapping as many Harpoons on the thing as you can, and vanilla Starsector is way too Harpoon-centric as it is. I'm having a hard time justifying a place for the Aurora in my fleet. This change is a net nerf, and the Aurora did not need a nerf. I'd recommend just changing the medium synergy slot back to a large missile slot. That would keep the AM-blaster build for the people who like that sort of thing, while still letting the Aurora be a viable missile platform.
I agree that missiles have power crept a bit too far. The AI is very liberal with the missiles when ships go above 80% flux; I would have had a great screenshot of the AI unloading what must have been 4 dozen Harpoons from 3 Enforcers, a Falcon, and a Vigilance in an attempt to kill my Doom, but this patch is giving me having trouble with screenshots. Starsector+ nerfs Missile Specialization, and that does make the missile situation feel quite a bit better, but it gives out Atropos racks to what seems like every pirate and Hegemony fleet in the game and that doesn't help much. The sheer quantity of guided strike weaponry the AI throws around is staggering. Not that I'm much better really, all of my destroyers and frigates get Harpoons if they can mount missiles.