If buildings are supposed to scale with the city instead of having to build multiple copies as in WoM, then perhaps the cost should scale as well. A combination of fixed and percentage cost to operate the building would level the income a bit, increasing early income and reducing late game income.
Apart from that, I think the best idea is to reduce troop cost when stationed in a city. Reducing stationed troop costs would make garrisons cheaper and more interresting than the automatic militia units, reduce steamrolling, and give you something more to do with your build queue.
I see Frogboy's point that buildings that give +X when the queue is empty allow you to get something when the queue is empty, and customize what that is. Building several different kinds could give you multiple bonuses when the queue is empty. The problem is that most of those buildings are city upgrade bonuses, so you make the decision once and can't change your mind later when situations change. Those buildings are also costing you money just to have, even when the queue is full, so they are pointless to build until you are basically ready to abandon the city's queue. Maybe if they only cost maintenance when the queue is empty, or did something when the queue is full?
The alternative is to have techs or even city level bonuses that allow you to build Trade Goods, etc. This alternative allows you to change your strategy as your needs change without having to rip/replace buildings. The down side is that you would only get one bonus at a time per city, but distributed over multiple cities, you could diversify your empty cities if needed. It would also require a little more work in queue management, but less work in planning empty queue bonuses for cities by building. The bonuses you get from empty queue buildings isn't all that visible. Maybe this is more of a UI issue.