How about having a factory bonus whose value increments (also decrements) by x units every n turns of ownership (like what is done for fatigue)? This could represent increased efficiency. Bonusus could then have a cap value as well. Anyone else see where this could come in handy?

I'm pretty sure it's possible to create what you are describing with existing factory functionality.  Of course, as with many of the advanced factory mechanisms, Abandon must be ON, which opens up a can of worms for many designs. This is yet another reason that Per Territory Minimums would be such a valuable designer feature.