I've started manually refitting mine with just PD (or nothing, mostly) - and replacing unnecessary high end shields/armour/reactor/engine so they don't use up rare construction resources. Even advanced cargo isn't really really necessary given that freighters are often nearly empty anyway.

Has it maybe got funny amounts for resource stockpile reserves?

Although role restriction seems more likely.

Do stealth cloaks affect resistances at all? They don't have a resistance listed, but they do take a defence slot.

(I've been putting one on most of my combat ships for the countermeasures bonus, but the thought occurs to me that I might be nerfing the ships' resistance)

Waiting for fighters to re-dock, maybe?

As far as integrating them, I've done that with pirates that liked me somewhat when I blew up their base, but I have not seen it happen peacefully. Did you do something in particular to trigger it?

Couldn't find a "spoiler" function, so just don't squint if you don't want to know :)

If you ...

It would be so much more fun if there was more actual diplomacy to be done with pirates, like actually having them do protection, and eventually integrating them into the faction peacefully. Maybe in the future?

I've not noticed them actually doing any protection, but if you keep in their good ...

Yes, once. I was repairing some ships in a debris field near a Mortalen AI station, and they went to the local Mortalen empire.

I assumed it was some Mortalen story-related thing breaking and just left the rest of the ships in that field.

But it will replace low tier missiles with high tier energy weapons if they are both standoff type - which I think is incorrect.
That does seem to be what it's doing for me. I agree it's not great though - e.g. I tend to put seeking weapons in slots with more limited arcs of fire, I might not want ...

Just to be clear, by "upgrade" I mean what the game is showing you as "Latest Component" in the components list.

When you actually click the "Upgrade" button to upgrade your design, the game will attempt (as far as I understand through my experience) to place the weapons that will give your slots ...

I don't think it's strictly fire type, although I'm not sure exactly what it is - e.g. researching Super Arrays deprecated my Plasma Thunderbolt torpedoes in favour of Death Rays. Hail Cannons and Ion weapons are still shown as latest though. :?

EDIT: Actually, it could have been in favour of ...

I wholeheartedly agree with the OP.

In my current game I had a long time to build up before I met any other races. So now I've met them, they all hate or at least dislike me from -30 or more envy modifier. In this playthrough I'd rather co-exist with my neighbours (or at least the 'good' ones), but ...