Hi Derek,
I hope you will consider giving the buildings the same kind of love. For example, my entry in the quest contest (which you did not accept) was about a sleepy merchant who possessed a seed--a seed that would grow into a gildar tree when planted in one city. This tree would grow and produce +1 gildar per level of the city. This is one example of a random/unique building that could be introduced by quests.
Another way to introduce cool buildings would be to give champions traits like cobbler (builds a clothing shop with specialized leg/boot armor not found anywhere else), trader (builds a market guild that can trade any resources for other resources), etc. Once those champions were recruited, they would give the faction the ability to create special buildings in all cities or one building per faction depending on the building.
Techs would also introduce new buildings but you probably already thought of that. Not all buildings would be available in every game. Thoughts?