It's a bit painful to see this mod appearing just 2 days after release to hotfix the issues Firaxis didn't notice... but I suppose creating a community-supported pseudo-patch is the best way to show them how to do things right.
First off, with the increased affinity level cost, is it even possible to reach max affinity without leveling the might tree?
With the trade routes, I would say 1 is way too low. How about leaving depot at 1, but giving the +1 back to autplant (or any other building/tech of your choice). I would even say that getting a 3rd trade route at a dedicated lategame tech (leaf, preferably) would be fully justified, given the internal trade routes are already nerfed.
As well, why did noone yet mention the Alternative Markets virtue? It adds 40 energy per turn to all sea trade routes to tier 3 stations and can be achieved before turn 100, causing an economic spike that just feels wrong. I even used station trade routes lategame, because even power-growing cities cant compete with the several hundred energy I got from that virtue (imho).
The wonders are, imo, a complete mass and need a rework all across the board. We got stuff like the Ecto Pod, which even the AI knows to priorize, and then stuff that just gives a +4 yield like some building. The only reasonable way of using most wonders seems to be combining it with the Knowledge virtue that gives +7culture per wonder. Which in itself is grossly overpowered if all wonders were to be useful, thus that needs to be adjusted, too.
As well, I have only gone into shallow water regarding CIV modding before, but how much influence can you take on the AI? Because I still think this is the most important issue. It keeps ignoring civilian units passing by their army at war, but is too dumb to even send a single unit to defend their colonist driving through my territory (AT WAR!).
Anyways, I've got a long list of possible bugs and suggestions, but I would wager most of them aren't able to be solved with mods. If you're interested nontheless, tell me and I can forward it to you.