Hi Ryan, It's somewhat difficult to price prototypes but I would say yours is worth at least $150, maybe more.  As far as differences between prototypes and the final release, it would all depend on the particular prototype.  Some differences are visible right away such as a title screen change or obvious sprite changes and some are much more subtle (text changes, sprite changes, etc) while some have no differences at all.  It you have a copy of GI Joe, I would suggest trying to compare the two side by side and see if you can denote any differences.