Did you change Yellow and Blue Nexus to take out the Garden upgrades and the Engine upgrades or to add prerequisites? All three tiers of each branch are missing as an option for me. Yellow Generators and Blue Mirror branches are there. I loaded a save from before the patch, and that save still has the others as options. I don't see this in the patch notes. Same custom civ before and after the patch (made in game, not a mod). edit: since I posted this I see that there is a new Red option (Coordinator Tree). edit: Turns out I changed from Devout and Empathy to Devout and Vigilant before and after the patch.
I found this steam forum discussion https://steamcommunity.com/app/1357210/discussions/0/601897008023733579/ and it has a list of civs and the nexus upgrades they get and later in the thread someone (seems official) said it's actually linked to traits. Is there a guide available for what traits match with what nexus upgrades? Did it change in 3.0 from what was posted here? Is it just the two main themes of the civilization that decide the nexus upgrades (e.g. Devout, Empathy, Vigilant, etc) or do the smaller options also help determine? (the options with +1,+2,-1,-2, 0)