The stumpjumper is made of higher end steel (whatever that means) for the rest they are the same... The Rockhopper is probably a bit heavier and less forgiving (flexible). I base this on the differences between my S-Works steel bike and my Rockhopper from the same age. That said the Rockhopper gives me more the feeling of a nuke proof bike that can handle everything!
It's that sometimes ineffable retro 'cool' factor. Stumpjumper's were perceived as the better bike, and no doubt still are, if you're out to buy a retro Spesh.