I actually thought the Smoking Man was handled okay but everything else about the Conspiracy ended up being too convoluted and sometimes just bad. The movie I have mixed feelings about. It felt like an end to the show but then the show just...kept going and they had to find a new alien plotline which seemed to have potential beginning with Season 7 but that too was botched IMO.
An excellent point regarding the movie. That should have been the beginning of maybe annual motion pictures, or bi-annual to expand the story. Instead they returned to television with diminishing returns year by year.