Commenting from a recent play-through and going by my own observations, my apologies if any of this information is wrong as I'm still getting to grips with everything.
I agree with the need for a buff to Martial plots, in larger settlements the need for them becomes too high
Commercial plots seems under-powered compared to the new advanced industrial buildings, with dynamic needs the total amount of Power/Water/Defense that becomes required to get to level 3 commercial plots (when counting the required level 3 residentials) seems not worth it. In comparison I seem to be able to keep my residential plots at level 1 while getting higher level advanced industrial at a fraction of the cost.
Admittedly this is partly due to me keeping residential plots at lower levels by choice but maybe there should be a greater benefit to getting residential/commercial to higher levels. Maybe advanced industrial plots should have a requirement for higher level residential and/or commercial existing before it will upgrade. Another option is to shift the taxes away from advanced industrial completely and increasing them from higher level commercial plots.
Maybe it's just my interpretation, but I don't think everything is meant to have a mechanical benefit for the player. The system is as much about making the settlements feel alive as it is about benefiting the player. So some things are purely a negative impact (like upgrading residential plots). I think if anything, higher residential plots should provide Happiness.