I have not been keeping close tabs on the details of all the various changes made since 3.15ish but a few things outside of barbarian uprisings (which you nailed explicitly!) annoyed me. keep in mind I have no idea what is a trivial code change and what is simply not possible.
1. Forests diagonal to river files were not receiving the +1 commerce to lumbermills like mills parallel. Yeah diagonals blow, but hard to really see the difference when playing. Really like hexes, sigh.
2. The deer event should really pop a deer resource instead of just gold (I think it was gold). Also the moose even that gave some food should get a resource pop as well imo.
3. Rivers generated to make city starts better would not create flood plains on desert tiles.
4. Ironclads should have an innate combat bonus vs 'wooden ships' which allows lower overall combat strength (pure opinion hehe). Like the added speed.
5. Those one tile off the river city starts, with a lake plopped down to compensate, are as annoying as they are frequent
6. The ability to force a coastal start (or land or random). Really doubt you can change this.
The overall mod looks fascinating as presented though, will give it a shot.
Cheers!
-Liq