The geometry will be different too, so whilst the stumpie is classed the better bike the hopper might fit better which IMO is more important than tubeset but the stumpy does have the higher retro kudos.
I've got a 93 Rockhopper and a 94 Stumpjumper, there's not a great deal of difference IMO. Like everyone says, the Stumpy would have been the more expensive bike when they were new.