I like Prison Break despite some of the aforementioned problems, but lets face it most shows all have similar problems.
Prison Break was originally written as a two season show. After the success of season 1 Fox realised they had a big hit and got the second season re-written to continue the show after season 2.
Season 2 really stretches the imagination of how all the various cons manage to escape and survive for so long. Season 2 lacks the closure it deserves. If it had not been rewritten so badly it would make a much better show.
Currently downloading season 3....
Heroes is the best TV show out there.
And Lost is a load of crap!