I like the new description for the Ion Pulser.
A few minor quibbles:
The Prometheus-class still uses PD drones as its ship system. Also the drones (both high-tech and midline, as well as Sensor, Terminator and Borer) still show up under Ship Systems in the codex.
The Flash Bomber's description states it uses proximity charges that "employs the principles of the phase cloak". Is this purely flavour or has the prox. charge launcher changed in some way? The description of the weapon itself doesn't seem to suggest any changes.
The damage type explanations for Energy and Fragmentation both mention hull damage, but it doesn't for Explosives and Kinetics. Given that hull damage is always 100% it's probably unnecessary information anyway, although might be worth adding it to everything for the sake of new players? Either way seems fine.
The Devastator Cannon's description keeps mentioning frag damage and how terrible it is against armour, but given it's actually Explosive it seems like it would be reasonable against armour. Granted I haven't actually tried it out yet, so it may be as terrible as the description keeps telling me.
Some variant hulls seem to be hidden in the Codex. E.g. Pirate Buffalo, Pirate Wolf. At first I thought they were deleted (Pirate Buffalo to be honest makes little sense, what's the point of a smuggler's hold and then painting your ship in PIRATE COLOURS OF DOOM), but they still turn up in-game.
Given the Terminator drone doesn't use a phase cloak anymore, should its sprite be changed to drone_terminator? The one without phase coils? Also minor typo in its description: "if orderd".
Is there a point to the Salvage Rig when the Shepherd has the exact same hullmod and is just generally a lot more useful?
The Harbinger's new description has a minor typo: last line of first paragraph, "Everything that can possible can wrong does".
There are no more Assault Fighters.
I get why this is with the new fighter changes, but the tab still exists in the Codex. Also some more fighters might be better under "Support Fighters" (e.g. Claw, and previously Longbow), as it is it's just Xyphos: unless Support Fighters are now only meant to be long-ranged support.