I've read it several times, tried my best to account to account for halo effect, and I still think HP:MoR is among the best things I've ever read. It may be that I simply need to read more good things. But it's pretty likely that I'd prefer good things that are more like HP:MoR, not less.
I do think it has flaws, both as literature and as a piece of propoganda (it's both, and that's fine).
If MoR is among the best things you've read, you need to widen your selection of literature.
This may be old news to some people, especially the Russian speakers, but I didn't see an article about it here.
In 1999, Kirill Yeskov, a Russian paleontologist, wrote The Last Ringbearer, a 270-page take on Lord of the Rings from the point of view of a medic in Mordor's dying armies who is also a "skeptic and a rationalist." In fact, Mordor represents the forces of reason in this retelling of the story. As a Nazgúl (himself a former mathematician) explains, Mordor is "the little oasis of Reason in which your light-minded civilization had so comfortably nestled." Barad-dur is "that amazing city of alchemists and poets, mechanics and astronomers, philosophers and physicians, the heart of the only civilization in Middle-earth to bet on rational knowledge and bravely pitch its barely adolescent technology against ancient magic."
The story has been newly translated and is available in free PDF form -- in English and the original Russian. There's a recent review from Salon as well.