Interesting comparison. Classic versus (IMHO) an under rated Stern. Funhouse has what a lot of people would say is a revolutionary toy (Rudy). Simple rules but there is a wizard mode. I find the game is left flipper dominated due to the geometry of the play field. Hitting the trap door shot is very satisfying. Rudy call outs are cool. My wife positively hated the game due to "Chucky". I have owned twice and most likely will not buy again.
X Men has a lot more shots, obviously it has the DMD dots ( Color DMD is a must as is Newton ball mod). The rules are actually pretty cool. In a family environment , X Men may be more desirable( it certainly will not get the possible "wife" factor ). If a great condition one at a real good price came up I would buy again. I do like the Stern "rules" games tho.
Agree on the "move" factor. X Men unless priced correctly will not move anywhere as quickly as FH.
I would make my selection based on price and condition.