I really like X-Men. It's packed with features. 2 voices are plain awful (Beast and Storm). Great combos. Made it to Dark Phoenix 3 times. Great wizard mode, albeit a little confusing. Very forgiving pin. Tough to beat wizard mode, but I thought it was kind of easy to get there.
Funhouse is obviously simpler, but iconic. To me, it put pinball "on the map". It's accessible to everyone. If the playfield particularly is in great shape, I'd take FH any day. Simpler code but still, the first game after I bought it, I got GC score and haven't sniffed it since.
X-Men is tougher to move. No one will walk in and say "wow you have an X-Men?" But code for X-Men is leaps and bounds deeper than FH code. I really like both games. Condition would be a factor for me, IF you plan on keeping them "forever" (that's in quotes on purpose, of course).
X-Men though doesn't have "deep code." It's more like "a bunch of stuff you have to do" code. Modes aren't deep. You're still trying to start something, and hit 3 shots max, except for the multi ball. You can try to stack a multi ball, but I don't think it's necessary. Wolverine is the toughest. Just a lot of work if you don't finish it the 1st 2 times or so.
I really enjoyed X-Men. You can stack and pair modes like LOTR or SM. Looking at your collection, I'd rather have SM Black than X-Men. They're kinda sorta similar. If you want code/modes/combos/features, it's X-Men.