In the current design, Mechjeb has the prevent jet flameout feature cut the throttle. This throttles all engines, including rockets, not just jets. This can be problematic on SSTO designs that call for switching on rockets while the jets are on their last leg.

Additionally, it would be even more useful if MechJeb could throttle back the engines that give the least thrust per amount of intake air used or least efficiency depending on the user's choice. This would help in designs that have more than one type of engine.