The main problem might simply be the long wait between the books. This strengthened the feeling that storylines won't get resolved and frustrated people (it seems a bit similar to A Song of Ice & Fire now). I imagine if you directly read all books in a row, some storylines might work much better and feel less boring to you. At least several people, who found CoT boring, described this experience after reading WH, CoT and KoD in a row. In retrospective I think all storylines had some merit. Of course, one could have shorten some things or even completely leave them out, but it's simply RJ's style to be on the one hand such detailed, one the other hand somewhat hesitant about revealing secrets.