i also noticed that Simon changed a bit. not only from his develpment over time but also from the pre-credits sequence: he almost looks like an action hero there and from the series that's the lastthing i would say about him!
also, i had the feeling in the series that Simon and Mal were becoming kinda friends but their dialogue at the beginning is pretty harsh. and i feel that in general the chracters have been neglected in favour of action, but i guess that they couldn't do much about it in a movie destined for the cinema.
and about the time line thing: from the story - especially if you consider the time Inara would need to settle in the school and Book would need to establish a mission - i would say that at least 3 to 4 months must have been in-between. but i'm not sure, haven't been paying much attention to that when i was watching it.