The basic metric their level generator used for quantifying interesting difficulty was the earliest point of non-trivial divergence in solutions. I.e. if there's a puzzle with a 50 and 51 move solution, having those solutions diverge on move 3 is interesting. Having them diverge on move 45 isn't.
https://web.archive.org/web/20100221131225/http://www.thinkf...
(The text of the article is only visible at the very bottom of the page for some reason)
Thinkfun & Mark Engelberg, "The Inside Story of How We Created 2500 Great Rush Hour Challenges"
https://web.archive.org/web/20130703141244/http://www.thinkf...
I'm not sure how best to assign probabilities, or how sensitive it would be to that. Perhaps uniformly, or perhaps biased toward moving closer to the end state.
The guy who made the website literally wrote his master's about it: http://code.ulb.ac.be/dbfiles/Ser2005mastersthesis.pdf
I'm interested in the "hardest" 6x6 puzzle. You show the one that takes the most moves to complete, but I don't think that's necessarily very difficult, if they're all pretty straightforward. Rather, I think the hardest puzzle is one where you have a lot of options to choose from. IOW, a very broad tree, rather than a very deep one. Are you able to quantify the hardest puzzle along those lines somehow?