There's this 'thing' that Whedon does in all his stuff (not counting Avengers) that pisses most fans off. He didn't get a chance to do this 'thing' in Firefly, so he did it in Serenity
This 'thing' is what Solo refers to as 'Bad Whedon'.
It is also why Firefly pretty much has to be viewed before Serenity, or it will kinda ruin the series for you.
As other's have noted, the tone of the movie is very different. Whedon was under pressure to produce something that succeded where Firefly failed, so he sci-fied it up, and pretty much eliminated the space western take of the series.
Conversely, Whedon claims that Fox made him tone down Mal's character in the show, 'cos he was too much off a bitter a-hole. Supposedly the 'darker' Mal we see in the movie is how he was meant to be in the show.
Imo, Serenity is a good movie, but not a good Firefly movie...