I've been doing lots of tests and without exception it takes much longer to export via media encoder than from Premiere Pro.
Since Media Encoder seems to spawn a headless version of Premiere Pro in the background, I don't understand why AME is sooooo slow in comparison.
This is on both Windows and Mac.
The time difference can often be double.
As an exmaple, 28 minute sequence (native Canon MXF 25p sequence) with colorista II applied to most clips takes around 90 mins to export from Premiere Pro but almost 3 hours in Media Encoder. This is WITH GPU turned on.
I never got a decent explanation for that, but I found that a simple SD PAL DV-AVI timeline with a length of around 90 minutes takes 17 seconds to export when using Direct Export, but takes 59 seconds when using AME queue. That is almost 350% slower. The only thing that Adobe came up with is the overhead of AME, but that is pretty lame and shows that code optimization is really necessary.