Megas, I was testing as Apogee as a fleet ship as I do small starts. I assumed it wouldn't be flagship as I tend to use phase ships as the piloted ship instead, but I can understand your reasoning.
I was thinking a bit more about the Ion Pulsar and I suppose a SO Medusa, like the Aurora is just about the only other ship than might want to use it as it can jump in and out with its Phase Skimmer. Looking at the ship variants for an insight to inteded role, only Aurora, Harbinger, Conquest and Paragon has variants with it. Aurora (Assault Support) variant is hilariously emp focused with 6(!) ion cannons and 2 pulsar, the Harbinger can have better layouts, and the other two will never use it.
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As a thought experiment, is there a mod that simply replaces all ships in the game with energy weapon variants? How much of a change in ship stats for Flux Capacity, Flux Dissipation, Shield efficiency and Speed is needed before turning a pure ballistic ship into a pure energy ship is considered equal?
On an assumption that "normal" energy weapons are a combination of a Kinetic weapon and High Explosive weapon which are always paired together with a 1:1 Flux / damage, the KE and HE ballistic weapon combined together actually have a 0.8 Flux / damage against shields. This suggests that assuming energy and ballistic weapons are equal (which they are not due to range, accuracy, weapon speed, armour effects), energy weapons should have a 0.8 Flux/damage, or energy ships should have 25% more flux dissapitation if otherwise exactly the same as ballistic ships.
Of course, neither weapons nor ships are otherwise exactly the same, and I've ignored armour effects where the paired KE and HE weapons will do better than a shield dps, but that energy weapons should have a 0.8 Flux / damage is a good starting point for comparison. For point of comparison, the IR Pulse Laser is 1, the Pulse Laser is 1.1 and the Autopulse Laser is 0.833 flux / damage.