Here's a proposal: let there be Ape populations on Earth or on naturally occurring habitable worlds. These apes can be genetically and cybernetically enhanced to serve as laborers or warriors, at great advantage, but if you let your guard down they go on rampages and/or enslave your human population on a particular world. The idea is that there would be a powerful temptation to use them for short-term gains, but in the long run can get out of control.
I have a related idea about cyborg ape cavalry with machine guns, but that would require implementing horses and stuff too, so you could save it for a later release...
