What we really have to judge this on is not the quality of the movies, but their geekitude vs. mass market appeal. Mass market is important in case you want to invite non-geek friends to the marathon. In this department, LotR wins hands down, though really, non-geeks seem to hate the Star Wars prequels much less than geeks. For some reason, we had inflated expectations.
Geekitude is complex in this case. Both have a high native geekiness factor, so it comes down to which one allows more "geeking out." Geeking out is defined as arguing subtle, even grossly insignificant, points of a subject in what is, ultimately, the primary social power struggle of geek culture. Debates are generally decided by proving more advanced knowledge of minutae. The winner basks in the admiration of his peers and the revulsion or indifference of present non-geeks, while the loser goes home and chews on his own spleen while re-reading his copy of The Silmarilion or some form of Annotated Screenplay to prepare for the next exchange.
The frequency of geeky marathons in these especially geeky franchises will ultimately be decided by which set of films provides the most fodder for truly geeked out debate.
Star Wars has a lot going for it: The debate over the quality (or lack thereof) in the PT vs the OT and the original vs Special Editions, the validity of the Expanded Universe material, whether Lucas really had a metaplot or has been flying by the seat of his pants, not to mention all the merchandizing material and Lucas' various positions on the nature of the film medium and his ownership of his "art" and ability to reimagine it, etc. All excellent opportunities to prove your geekhood.
But LotR creams it.
Just keeping to the movies, there are the differences between the theatrical and expanded versions. There is the wealth of geekhood inherent in the extra discs of the Expanded sets. Once you bring in the books, it becomes a geek out extravaganza. Comparison of the book to the movies and debate over the changes is just the beginning. These are broken down already on plot, theme, and filmability merits, and it promises to get more detailed as time goes by. The possibility of a live action Hobbit will be the stuff of internet gossip for years, I think. And the filmability of the Silmarillion will, of course, be debated. The impact of the Appendices and the Silmarillion on the films, the literary value of Tolkien's work, in and of themselves and as fodder for movies, the success of LotR as an adaption of the novel vs as a film in and of itself.
There is so much potential geekiness and fodder for the endless debates that geek culture seems to enjoy that the Lord of the Rings is the clear winner in this struggle. But I expect some of you will debate me.