KSP 0.23 is getting close and in this video it can be seen that the max throttle of each engine can be changed/controlled when building but also during flight. If controlled properly you would be able to control a VTOL much better without having to use PWM to alter each engines effective thrust.
I know that 0.23 is not out yet. But I would already like to add this suggestion to possible functions of kOS in the future.