Well firstly CM10.1 was built from AOSP source, while the GE build was created from the software on the GE edition HTC One, which is actually built on sense framework.
As far as functionality wise, there is just much more customization and functionality on CM 10.1 that isnt present in stock aosp android, I cant even start to list the additions, but there are a lot. There site
HERE lists some of them. Ultimately though CM is just nightlies for the time being, meaning its not 100% stable right now. The GE rom is much smoother obviously because it was built by the guys over at HTC.