I would like to discuss the relationship between factory and workers (in strategy games). The output should depend on both, the factory (building and tools) and the workforce (workers). I have a big trouble making a system where these both are important.
In Tropico 4, the people also develop skills in each job they work, and better skill translates to higher production.
Here's an idea: Make the workers the thing that gets the production accomplished, and everything else is a tool to assist them. Then a Factory is just a container for workers, which might have an upgrade-able population cap. A factory might also offer some sort of investment options as well -- sink an up-front cost into additional features, and the facility gains a bonus for everyone that works there.