[Pitchwife]

I can't claim to be an expert on animation, so I won't go into the technical questions that POTH has commented on quite competently, as far as I can tell. From my point of view, the rotoscoping works best on such scenes as the early confrontations with the Black Riders, the fight with the Orcs in Moria and to some degree the tide of evil in the final battle at Helm's Deep, to which it lends a somewhat surreal, 'otherworldly' quality which I quite like; but I agree it gets rather weird in the second half of the film.
(Which reminds me - when I first saw the film in cinema back in the winter of 1978/79, I was on the eve of coming down with the flu and got rather feverish during the viewing, so I actually wondered how much of the weird visuals in the later half might be due to my rising temperature. A rather psychedelic experience!)
And Leonard Rosenman did a great job on the score, as far as I'm concerned. The main theme is touching and unforgettable, as are the dirge for Gandalf in Lothlórien and the choir in the final battle scenes (if you listen closely, you'll notice that for want of better lyrics, he had them chanting his own name backwards - 'Namnesor Dranoel'; quaint, but it works!).
As for Bakshi vs Jackson, I'll be the first to admit that PJ handled a number of things much better - such as presenting Boromir as a likeable character who just temporarily succumbed to a temptation to strong for him, and Sam as the hero he is rather than a comic potato. (Even the Rankin/Bass ROTK, abominable as it is in many aspects, brought out the heroic side of Sam better than Bakshi - but then again, we don't really get that much of that side of Sam in the parts of the book Bakshi covers.) I guess the root of all my qualms with PJ is that he came so damn close to getting it right in so many ways that it hurts all the more when he messes up and gets off on some completely gratuitous nonsensical tangent.
Which finally brings me to another point in favour of the animated versions (even the R/B ones, I'm afraid). All adaptations of a work of literature in a visual medium - whether mere illustration, animation or live action - influence and limit our own imagination of the characters and events to some degree; and just as illustrations are, in this respect, less 'harmful' than movies, animation is, in my subjective view, one step further removed from pretending to be 'the real thing' than live action, as we're more conscious of looking at everything through someone else's artistic filter.
Looking at it from a slightly different angle: Michael Moorcock, in his rather blasphemous essay on Tolkien 'Epic Pooh', claimed that Tolkien was so successful because we, the readers, are actually much better writers than the Professor himself was and make up for his literary shortcomings by the use of our own imaginations. This is not the thread to debate his statement as far as the books are concerned, but I think it applies to the films in a way: in our minds, we're all better film-makers than Bakshi, so we can flesh out the gaps and smooth out his mistakes while we're watching and still enjoy the show. With a live action movie like PJ's, we don't have that much leeway to exercise our own imagination, we depend more on the film-maker to get it right for us, and are more disappointed if he doesn't. Or that's how it seems to me.