After playing around with the new version, some random thoughts on traits from me:
Still not satisfied with
Mercantile. I've come to the conclusion that the trait really doesnt work well - if you balance it for coastal starts it gets completely useless on non-coastal starts. If you balance it for the latter it is vastly overpowered for coastal starts. You'll get 4-5 Hammers and Food as early as early mid game. My suggestion is to either scrap the trait completely or change it completely. Two options I thought of:
a) Make the bonus dependent on the number of land tiles in the BFC. For instance, give 1% bonus per land tile. This prevents exploiting the trait which is easy to do right now (you can build cities wherever you want, even on 1-tile-islands, as long as maintanence costs allow expansion). And of course it will make inland cities better suited than coastal cities, which balances nicely considering the trade route enhancing buildings you can build in coastal cities. Historically speaking, it represents the boost to economy cities gain from the land and villages in their surroundings.
Of course, I have no idea if it is possible to code this.
b) Make the bonus independent of the commerce you gain from trade routes. Make it instead dependent on something that is (mostly) independend from coastal or non-coastal. It could be the pure number of trade routes a city has. Or, maybe better, the size of the cities it has trade routes to. For example:
Combined size of trade route connected cities /// bonus
15 /// 1%
30 /// 2%
45 /// 3%
60 /// 4%
80 /// 5%
These are just random numbers to illustrate the idea. Coastal cities would still be better since you get more trade routes and get them more easily, but to a lesser extent than it is now - no harbours, no custom houses, no overseas trading bonus. And the bonus mostly scales with time and does so at a slower pace. So you dont end up with the maximum bonus as early as in the middle ages.
That's my ideas for Mercantile. I hope you find some of it useful. As it is now the discrepancy between coastal and non-coastal seems an unbridgeable gap to me.
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I am currently trying to exploit
Diplomatic with an espionage/cottage economy and I am surprised how well it works. With the defensive bonus you added the trait might be fine as it is. The only minor problem I see is that both of its buildings only help espionage and will probably only be built if you focus on espionage. A small non-espionage bonus like the Jail has might help here. But I don't think it is necessary, just a nice little boost to make it more appealing to non-spies.
Strategic,
Agricultural and
Scientific seem fine as they are (though admittedly I haven played much with Sci). I found that I like Agri almost the most of your new traits (except Merc...) as its early boost is significant. Depending on your starting location it potentially boosts growth and production and research. Thisis highly useful! Double production speed for Granary would make sense, but it is already taken.
This leaves us with
Nationalistic - a trait both my friend and me are very underwhelmed by. Two of its bonuses mainly counter war weariness. The problem with this is that we almost never experience war weariness anyway. Even when going for a domination victory this never was a big problem. Personally I usually go with Police State anyway, my friend never does - but if he gets some unhappiness it is only like 1 or 2 citizens not working and only for a short time - and this only happens in mid to late game, vitually exclusively when cities are 15-20 big and you choose not to use emacipation while others do. No need to deal with this, it is insignificant. So in short, 2/3 of this trait's bonuses arent bonuses in our games. Suggestion: Scrap the -25%

bonus and replace it with something like "no unhappiness from drafting and emancipation".
Overall I think your traits work very well and only need minor tweaking if any changes at all. The exception is Mercantile which I think is broken.
