I agree that the first six books are the best - they were constant companions during my teenage years, even after I discovered "better" writers. The later books.... Well it's like checking back in on old friends. They may not have done much with their lives, and you may not be particularly interested objectively, but it's just nice to catch up and spend some time with them.
She wrote herself into a bit of a narrative hole with the main timeline, and the avenues out (Dolphins, All the Weyrs) weren't half as interesting as the original scenario, then she started jumping back to fill in the story from the perspective of other characters (Masterharper...) or earlier points in the timeline.
She went back and filled in the earliest storys of Pern, then the Todd books were set in a mid-point so they could make use of the main threat (Thread) without interfering too much with her own books. I haven't read them, but I've heard they are on a parr with her own later additions to the timeline.