Thought I'd share my point of view.
So, we're about half way through season 2, and I must say I am a bit perplex... Although a few episodes are really intriguing and have good turn of events, most of them are just confusing. I am starting to wonder if the writers wrote the show as the episodes went on screen, or if there really ever was an originial script to start with.
It just feels like the authors do whatever they want with the characters, put them on the case, take them off the case, put them back on the case, etc... to be able to introduce temporary new characters, and let Scofield get away everytime. But it just seems less and less credible as we go, how can Scofield get any smarter than he already is, how can he still get out of all these situations? What are the extents of the conspiracy they are a victim of? What are they going to come up with next: maybe the president of the US is an alien who wants to destroy the entire human race, so he chose to start with Burrows... whatever... Yes, the writers could be that twisted really.
Plus I think the show is flanked with awful actors, cf the actress playing Veronica Donovan, where did they find her? Thank you for finally killing her off at the beginning of the second season, she was probably the dumbest lawyer character ever seen on TV! She did exactly everything wrong, or everything to be caught. Also, The Lincoln Burrows and LJ's characters are sadly portrayed by the worst actors left in the show right now, and it just feels like their roles were written to have them arrested (because they're stupid, and all they do is so stupid!).
There's a great duality to this show: uninteresting characters (V.Donovan, L. Burrows: although he's the center point of the show!!!, LJ...) played by awful actors, vs very cruel criminals and tortured FBI agents who end up being the "cool" characters, because they actually bring something to the story and not only make time go buy. The only point to this season is the introduction of the FBI agent Alexander Mahone (played by the great William Fichtner) in a two-faced character with dark issues. And T-bag is as creepy as ever. Too bad they killed off the maffiozo John Abruzzi... why get rid of the good actors/smart characters?
It was way more interesting (and credible - if that's really possible) inside the prison! (So, season 1).
I just can't imagine what will be in Season 3. With Shad we're just really wondering where the action will take place: back inside the prison? Knowing that probably by the end of Season 2, all the escapees will be dead... No way to know, maybe we'll have more hints at the end of this season, but then again, it would mean watching the rest of it, which we're not sure we can do...
And on the other hand, we've started watching 24, that's why our attention is drifting I guess...