I'm really enjoying having combat slowed back down with the skill reworks. As a bit of a knock-on effect, it might make Phase ships a bit more reasonable; it's harder for them to instantly gib ships by themselves with less officer bonuses to damage output, and longer battles in general mean their limited endurance is more of a liability.
It also probably helps that they're much rarer opponents. Given the number of basic combat rules they get to break, they work better as minibosses than something you are liable to encounter in every other Tri-Tachyon patrol. I still don't like that the appropriate response to them is usually just to huddle in a ball until their CR runs down, though, because even if it works it's not fun or interesting gameplay.
Also, it's looking like the distinction between Pirate D vessels and regular D vessels is indeed causing quite a bit of confusion for the people who don't read the game forums. I accept that weapon mounts can't be refurbished for technical reasons, but is there any similar barrier to just calling it a Wolf (P) instead or something, especially given that you have already done this for Pather ships? On a similar note, is Destroyed Weapon Mounts on the table for random rolls? Because if it is, I'd probably argue that it shouldn't be as long as it's irreparable damage. If part of the purpose of the new salvage mechanics was to improve access and retention of rare ships, having a chance to have them be randomly crippled runs counter to that design without adding meaningful amounts of depth to the salvage system.
Refurbishment costs also seem excessive. I understand that refurbishment is primarily meant to be a way to gain access to ships that can't be bought with money, but it doesn't need to anywhere near the current level of expense to accomplish that goal. If a ship is readily available off the market, it doesn't matter how many times more expensive it is to have it refurbished; as soon as buying a new one becomes the cheaper option, that's what will be preferred. Paying six figures to have a Tempest rebuilt is...harsh.
If anything, I'd probably want to see the price for having a single D-mod removed at somewhat less than the price of buying a new hull. This still leaves refurbishment the more expensive option for the vast majority of ships you recover from enemies because they are usually going to be in worse shape, but it provides a mechanism for players who aren't running junk fleets to keep their ships in peak condition without constantly replacing their damaged ships with new hulls (or mashing F5), and maybe helps them feel a bit more connected to the ships in their fleets.