Obviously trade routes need toning down. About a third of the yields they give right now should be more balanced. Still giving more than buildings and improvements in terms of resources for having to defend them. An internal trade route really shouldn't be giving a combined resource (food and production on both sides) of up to 20 for a single cheap to produce unit. Easy enough to change.
Next I'm finding forest utterly useless. At best they're a neglible production boost, at worst a nuisance. Given how the new world is supposed to learn from the mistakes of the old, harmony players especially would be concerned with preserving the planets ecosystems, so I want to tie them in with health somewhat like in civ 4. Maybe I could change xenonurseries from boosting xenomass wells (because seriously 3 building to boost xenomass wells is just too much) to giving one health per forest tile. They'd give lackluster resources but useful health. Might need to make xenowells and biowells not constructable on forests to balance it out though.
Hills are a problematic terrain due to its low yield which is supposed to be counterbalanced by the high yield on standard mines, but this doesn't work when you have resources ontop of hills which end up being worse than resources on plains, having one more yield overall. One more production for hills and one less for basic mines means more flexible improvement options for hills.
Specialists are utterly pointless unless your city has next to no useful tiles in its range (in which case why place a city there
). Not sure what to do with those, maybe I can decrease their food consumption so you can sustain more of them, and thus more science in trade of lower yields? Right now there's not use for them as basic unimproved tiles are just as good.
And obviously a bunch of cultural traits need balancing, the investment trait especially. I'll worry about those later.