That's looking pretty good. Nice work.
The relatively low Move of the scouts (considering their purpose) jumps out at me as something in need of correction. I'm also not sure if having flying scouts be basically strictly better than land scouts is appropriate- for any other unit type, the Flying special would cost points instead of effectively granting them. It's a little awkward to modify units at this late date, but I don't think it would be inappropriate to tweak them so that there's only one Scout unit, with base move of 8 or so and the option of buy the Flight and (Terrain) Capability specials using its 4 points.
You have the Frightening special listed twice.
You might want to check up on the updated Burrowing description
to be sure that it's in line with what you've got there.
I believe the Battlecrap special is D-Class.
You may wish to put the rules on warlord promotion next to the rules for knight promotion.
You may wish to add the unique specials that various sides have developed for this game. While they may seem very side-specific, with enough games played we'll develop a wide library of abilities to choose from and the side-specific nature will become less important as they fade into a large array of options.
I am not sure how to balance the Improved [Unit] and Improved [Stat] city abilities. At the moment, the former can provide either stat increases or specials, but I don't think the stat increase to a single type of unit would be balanced against a blanket +1 in a specific stat to all types of unit. Restricting the available specials to Simple-only doesn't really help, either, and I'm not sure it's sensible; specials vary enough that it would likely be better to have the special in question and the % chance of popping with that special both subject to player-GM negotiation. It's less mechanical, but then city customization is producing things unique enough that I think player-GM communication at some point is desirable anyway. Of course, Improved [Unit] for the stat boost might also be best discussed with the GM- boosting a class D unit should logically have a more profound effect on its stats than a basic infantry unit, simply because its stats are higher and thus deserve more of an increase for the benefits to remain proportionately worthwhile. The cost of the city upgrade might be varied a bit to reflect the particulars here as well.
Your rules seem to lack stats for rulers, heirs, warlords, casters, and courtiers. Those should probably be included. I would appreciate a description of courtiers' specific capabilities as well; my impression at the moment is that they're basically warlords who don't have impressive stats and don't provide a Leadership bonus, which is to say, they're Commanders and can stop your units from auto-attacking but are pretty worthless in actual combat and generally have no specials worth noting.
I would strongly encourage you to use a chart of some kind for city stats. Having them all written out over multiple pages is unnecessarily cumbersome and makes it difficult to identify the costs and benefits of upgrading at a glance.