Could we get an option to throttle down lower ISP engines first when limiting thrust (eg limit to terminal velocity, limit acceleration). I have a feeling this is now possible using the Thrust Limiter tweakable during flight. Obviously not for SRBs. Might cause problems on imbalanced craft but that would be something the user should control.
Speaking of unbalanced craft, could the thrust limiter tweakable be used to balance thrust on unbalanced craft like RCS thrust can be in mechjeb?

Differential throttle support seems to address the latter part.

Maybe there's a feature request here for having the ThrottleController target certain engines only or have a throttle priority. That could help with the throttle down of center core engines in #951, but this feature seems like it might produce a lot of spaghetti code.