No matter what, Prison Break was never intended to be a long-running series. At first, people behind the show though it could last three seasons being laid out as follows: Season 1 = in prison, Season 2 = on the run, Season 3 = back in prison; but that the best plan was surely only two season. However good ratings have made FOX order a third season. With how they mapped the second season, which includes wrapping up most (if not all) of the storylines, Prison Break needs to reinvent itself and here is how they plan to do it.
Source: Prison Break’s third season to get a new name? – TV Squad
I love the show, but I do get the sense it would be better if there was a solid plan for the story arc and the networks could stick to it regardless of the ratings.