fishing boats - I want a reliable food source. An unreliable trickle isn't going to cut it. Either make it reliable or remove it. Aquaculture is a thing, so I'm not worried about the reliability of fishing.
Disease - The ramping up of curing rates is too complicated. Just have the initial outbreak be proportional to infection rate and have cures work at 100%.
District Limit - 1 + Social/2. This seems a little low, but we'll see. X + Social/2 is sounds more reasonable.
Shallow Mines - Just call them mines
Crime Building count at 300+ buildings - I still think this is completely unnecessary.
LImited Range Scouting - I've always hated this. It adds complexity (is it within range). It doesn't really add much to the game rather than needing to bulldoze and rebuild the scout stations to expand their reach. Now, if you made scouting range proportional to transport range + X, that would be more interesting. Then I can just leapfrog helipads and teleport stations and my scouts can start their journeys from there.
Building Counts - So much effort has gone into this, and I still dislike the entire mechanism. Population Count or Total Tile Count should be sufficient.
Planetary Rage and Monsters - I still think generation should be roughly 100 fold what is now.
Turn order - I need to break open the end of turn logic and parse that function out, but I still think it will help.
RAM - 3 gig is more than enough.