I could be wrong, but I don't think there are any true ebook reader apps that handle pdf (which is a terrible format for ebooks since it was designed to reproduce the layout of an original hard copy and does not translate well to small screens). Repligo is supposed to be a good pdf viewer, but if you want to take advantage of the capabilities of a real ebook reader app, conversion is probably the best option.
What is Calibre doing wrong? You might be able to get help over at Mobileread - there are lots of Calibre experts there.