After you get past the first couple of episodes for season 3 of BMS, Frankie James who played Mary Jo was removed from the opening credits and basically only a recurring character by the end of the season. Actually wasn't even in the 2 episode season finale cornfield game episodes to end the series.
I think it was because Mary Jo (as well as Radon) was added to the show in the first place because of Sam Jones III getting arrested, causing Shilo and Denise to be written out. They likely had to re-write whatever they had planned for Season 2 and work these new characters in somehow, thus creating sometimes unbalanced season. So with them being able to plan out the third season, they practically completely dropped Radon, minimized Mary Jo's role and were able to focus on the story arcs again.
Here's the long answer... we shot the show in Montreal, QC partial because when we started in 2009 the US dollar was really strong against the Canadian dollar and we saved money shooting there. But by the time we hit our third season, the US dollar had tanked and we were actually losing money by shooting in Canada. Because of this the studio asked us to make some difficult cut backs on our budget and unfortunately, Frankie Shaw's contract ended up being one of them. We fought to keep her on the show because we loved her, but the best we could do in the end was to get her into a couple of episodes. It was a tough loss, but if we hadn't made those cuts, there wouldn't have been a third season at all. Frankie will definitely be in the movie though.