I feel like there is room for a proper original theme but only if there is internal passion for it. Stern employs a lot of creative folks that I'm sure could excel if not limited by a license and pre-existing characters/ideas. For example, the team that did the animations for BKSOR nailed it, in my opinion and you could definitely build up more of a story with what's there. And for a pinball machine, the actual "story" really doesn't need to be overly deep and it could be catered directly to pinball much better than a pre-existing story.
But ultimately, the reason we see so many licensed themes is that a lot of people are just more willing to buy a machine with a theme they already love, sometimes sight unseen. Additionally, it's much easier to overlook gameplay, layout or artwork deficiencies when you are attached to the theme itself. So the question is, how the hell do you make sure you sell an original themed game? Since no theme, licensed or otherwise, appeals to every pinball player or buyer, I'd suggest that making a good game is the first step. Or maybe the real solution is to have someone like Elwin or Lyman attached to an original theme.
But then again, why would Stern take the risk when their current strategy seems to be working just fine.