Interceptors will indeed stop the pulse cannon and missiles but will have no effect on the secondary weapons (which are mini-beam).
Hull 6 vs. Hull 5 - you could change it Hull 5 but I suspect you're going to have to raise the hits to something in line with the Artemis AND increase interceptors! I wanted the stats to reflect the tech level of the crusade era (specifically the nemesis) hence the trait-heavy stats but I don't think it's especially uber-powerful.
One risk that I didn't spot would be the tendency to use them as JPB's - anything with AJP (esp at lower priority level when fighting high priority battles) will have this risk. Could change that to JP instead - main reason for AJP was to reflect it was a "high-tech", multi-role and rapidly deployable ship.
(Slight aside but personally, I think the JPB tactic shouldn't feature, AT ALL, in the game because it so open to abuse and appears in ONE film (I think) - hardly justifying the common use of JPB in almost every fight I've had that has allowed them.)
I like the idea of missiles vs. flights - you could have a variant that removed the missile and added flights instead maybe something like this:
Pegasus - Light Carrier Variant - Skirmish - EA Crusade Era
Developed as a technology demonstrator for what would later be used to construct the Nemesis class destroyer, the Pegasus Frigate was designed to be a well armored, fast and powerful skirmisher to act as a rapid deployment vessel with a "multi-role" capability, able to make EA presence known at the furthest reaches of it's domain. This early variant had much of the advanced armour plating removed to add modular fighter bay launch sections. Unfortunately, integrating these additional systems and crew quarters led to many compromises with the proposed upgrades to the ships computer and navigation systems.
Name: Class/PL: Pegasus - Light Carrier Variant / Skirmish
Crew Quality: Troops: 2
Speed: 8 In Service: 2266+
Turns: 2/45º Craft: 1 x Thunderbolt
Hull: 5 Special Rules: Jump Point, Interceptors 1
Damage: 16 / 5 Crew: 18 / 5
Weapon Range Arc AD Special
Heavy Phasing Pulse Cannon 12 F 2 AP, Double Damage
Light Multi-Phased Cutter 10 P 2 AP, Mini Beam, Twin-Linked
Light Multi-Phased Cutter 10 S 2 AP, Mini Beam, Twin-Linked
Particle Beams 5 T 4 Anti-Fighter, Weak
Really hope to see some updated piccies of the model soon too btw!