This is an interesting topic. I think it depends on who the target market is at a particular time. There was a time when pinball machines were the attraction. People would go to the arcade just to play pinball machines and other arcade attractions. They knew what they were doing, they wanted to get high scores and replays and extra balls. The left their homes with an intention to drop some money into a pinball machine. At times like this I don't think that licensed themes are nearly as important as gameplay/rulesets.
When Bally/Williams shut down and Stern was the only kid on the block times were very different. I think for the last 10+ years (or more?) the most common place to find a pinball machine on location in Ontario would be at a movie theatre. These are locations that people(mostly kids) were going already, and just needed something to do to kill some time. In situations like this, I think licenses themes are king. Kids are going to see Spiderman or Batman on the big screen and see a fancy flashing box with that theme painted all over it and think it looks really cool, so they drop a couple of tokens in it. Generally these are people who know absolutely NOTHING about pinball, replays, extra balls etc. I think this is very obvious when you look at the condition most of these games are maintained to. The avid player doesn't want to play a game with broken features/weak flippers.
We're certainly seeing a change in times now. Gary Stern never even considered collectors as one of the legs on his "sales stool" until only recently. Collectors are now a big chunk of the market, and the avid player is making a comeback. When it comes to these types, licensed themes aren't as important, which is why we're starting to see some unlicensed themes popping up.
The bottom line is that I think we'll continue to see mostly licensed themes. They appeal to the masses. And as a blanket statement, a lot of collectors don't care about the theme (e.g. BSD, JM, TS) and it won't hurt sales if the game is good. I know personally I would never purchase any ACDC or Metallica collectable material, or t shirts, but I would have no problem having those games in my home because they are fantastic pinball machines.