I've had my 2012 Retina MacBook Pro for just over three years now and have been noticing some weird slowdowns in the past few months, especially if I was running a VM. At first I was blaming it on Parallels or El Capitan, but then was noticing it happened with other CPU taxing apps. If one did any kind of sustained load on the machine the fans would ramp up and the machine would get slower and slower with kernel_task taking a larger and larger percentage of CPU time. It didn't even have to be a heavy load, just something that was a constant drag on the machine. Downloaded Intel Power Gadget to see what frequency and temperature my chip was running it. These chips are all supposed to be able to hit around 100 degrees Celsius before throttling kicks in, but I would see the frequency drop down to ridiculously low numbers like 0.8GHz (on a supposedly 2.6 GHz machine) while under load and yet the temperature was less than 80 degrees. The fans however were going at max speed. Took 20 minutes to open the underside panel of the Mac and blast compressed air outwards through the back and side vents. These vents are tiny and it doesn't take much dust over three years to block them. Hold the fans to prevent them from spinning and turning into unwanted generators. Ideally just get the Apple Store to do it for you if you have one nearby. I tested the results before and after cleaning by running Prime95 for 5 minutes and then recording the CPU frequency. I also recorded how quickly the fans slowed down after Prime95 was stopped. If airflow is good, the fans should be able to quickly get rid of the lingering heat and then slow themselves down. And I got dramatically better results! On a heavy workload the frequency went up from 1.7GHz to 3.0GHz, and once it was finished it took less than a third of the time for the fans to return to effectively silent. Graph of before/after frequency and fan speed attached. TL;DR: If your Mac throttles even though the CPU temperature shows it should still have thermal room, it might be that your vents need a clean. If the vents are blocked other parts of the Mac heat up and the other temperature sensors will kick in and throttle the CPU to protect the overall system even if the CPU itself isn't in danger of overheating.