[Captain Kwok]

This are primarily SE:V issues, but some of them I can address (most of the treaty items) via the scripts. The counter-proposing treaty or amend treaty options I believe are two diplomatic actions where the proposing Empire's name is invalid and therefore appears as blank. I had meant to fix that for v1.02 but forgot about it.

I haven't touched Alliances so they are just as screwed up as in stock. Eventually this part of the game will be addressed by the mod.

The load a game from a game image error was actually fixed previously but somewhere around 1.1x it got borked again. Running the turn though will restore the images.

No retrofitting/mothballing in fleets is intentional - although you can retrofit a fleet of the exact same ships. I also believe you can select multiple ships of the exact same type to retrofit as well. Anyhow the lack of a retrofit window like in SE:IV certainly makes retrofitting more tedious in general.