Quoted from MikeS:
Instead you have RS, which sells for under $2K despite a production run that is only about 40% of what it's predecessor "TZ" sold.
People might not know this, but a big reason that RS probably sold so poorly was that TZ was a total route dog. It broke down constantly, and people didn't understand what the heck they were doing on it. When I first started in pinball, you could regularly get nice ones all day for $1500 or so. It wasn't until repro parts made them totally repairable, and people figured out that it made a great home game (if you like that sorta thing) that it's price went up.
So it depends on what you call a flop. TZ was a route flop at the time, but it sure doesn't seem like one now. And IJ4 which a bunch of people mentioned apparently does really well on route from what I've heard.
If you're looking for games that didn't sell, the only recent one that seemed to be blown out has been WoF. Before that, there are lots of stories of games like CV and CC being blown out for like $1500-$2000 NIB because people didn't want them. Time changes the perspective of flops rather dramatically.