The ascent module throttles back if an engine is overheating. What would be fantastic is if it would also throttle back if a jet was running low on intake air, and if an ion engine was running low on power. It seems relatively straightforward to add driveLimitIntakeAir and driveLimitElectricity to MechJebModuleAscentAutopilot.cs though I don't know the API well enough to see how to find the information required.
Even more fantastic would be to split out the auto-throttle and add it to, say, SmartASS.