Why is Adobe Media Encoder so slow?
10 times the length does sound pretty long, but isn't completely insane, particularly if you are running two pass.  The more compression you are trying to do while maintaining quality, the longer it is going to take to compress it down.  

It's also possible that if you are using nested projects, it may still be trying to do some rendering at the native resolution of the output for it.  Are you running the MP4 or the project through encoder?  If you have a full res MP4, I would suggest trying to run it directly instead of running the project.  The quality will likely be lower, but it should run a lot faster.