Yes there are inconsistencies (most of which can be explained "in universe"), but they really come down to transitioning the story from television to film.
Whedon needed to sharpen Simon's backstory and make him much more pro-active in the movie, hence the noticable and sometimes jarring changes in the good doctor's demeanor. But his appearance was also noticably different. The television Simon had a boyish quality; his hair was tossled and he dressed in foppish Western attire, as if his mother had picked out his clothes for him. The movie Simon's hair was slicked back and the Western garb was gone. He looked "harder", more utilitarian. Either "foppish" Simon was an act (not an inconceivable idea) or Whedon did indeed retcon him to move the film along.
As for Mal, it was mentioned upthread that Fox thought his portrayal in the pilot was too dour, wounded, and grim. They wanted Whedon to lighten him up, hence the Mal we know from the series. When given the chance to make the movie, Whedon returned Mal to his original concept. Indeed, the Mal Reynolds in the two bookended "Serenity" films (pilot and movie) are the same guy; it's the television Mal in between them who was different.