If I were an actor and played a main character, I would like to have a say about how my character should develope and act.
But not everybody are like that. In certain rock bands there are one or two members who write the songs and set the standard for the band while one or some member just tag along. I guess it's the same in a bunch of actors. There are those who are coming up with ideas and those who are satisfied which just playing a character no matter what.
But if someone is kicked out for that, despite doing a good job, then something is very wrong and obviously those in charge didn't listen to everybody either. Robert Beltran did have a lot of ideas for his character which all were ignored by those in charge and that was a reason why he became very dissatisfied with the series. As for Dawson, they obviously didn't listen that much to her considering how her character were shoved in the background in the later seasons.
As for budget issues, if the budget was so tight, then they shouldn't have made any changes in the cast att all. Instead they should have done their best to write the best possible stories for the excellent characters they already had.
They could also have made some cuts in the budget by not using some of the recurring characters as much as they did. I don't think that the actors who played Vorik, Naomi Wildman and Icheb worked for free.