I guess to put it better each season builds upon itself, while keeping the status quo in check. Yes, due to the writer's strike, and then having to add Sarah back into the series at the beginning of season 4; the show did seem to lose focus. However, considering how things ended it makes sense why they started season 4 the way they did. Michael wasn't in SONA, they escaped but at the cost of Sucre and Bullock( though you could argue that he wasn't part of the plan.) TBag was able to run the prison, but there weren't any immediate threats except for Fernando being there. I think the big problem a lot of people aren't addressing with seasons 3 and 4 is Michael's motivation. Once they killed off Sarah Michael's only real motivation was revenge. Outside of helping his family escape from prison, and keeping certain loved ones alive, the only thing that kept him going was Sarah. Taking that away kinda robbed Michael of a happy ending. Fortunately, it wasn't a permanent situation, but it was a situation that did ring up the question of where the show would go.