From talking to builders not much other than the available colors of the factory painted finishes. You probably should also look into their warrantees. I've researched them both and they both seem to have had their problems but it sounds like if properly installed they are both good products.
Also, here is an article on the differences, but I can't attest to the author's bias if any.
http://www.exovations.com/blog/?p=246

I would steer away from the pre finished siding they have limited colors and you have to make sure if you do get the pre finished siding that the siders are skilled to handle the siding it scratches easily it doesn't touch up well ,