It was definitely the SHU they were putting in him, no doubt about that. I agree the ending was good although I found someones thoughts over at
Prison Break Manhunt brought up some concerns about it though, although he is been abit critical. Anyway I was compelled to prove my point about Fox River so I went back into my archives and took some shots, looking back at it, the scene zooms out in the exact same way it does in the Pilot as it does in Killing Your Number. See the screens below ;).
http://www.jettmedia.com/images/603_foxrivers01e01.png
http://www.jettmedia.com/images/716_foxrivers04e22.png
I'm pretty sure it was Fox River, when it zooms out is shows the same layout and rooftops we saw in Season 1, pretty sure of it anyway. I guess your right, Sara still isn't free and neither is Linc now seeing as he helped her escape, same goes for Mahone and Sucre if they get the evidence. Although I suppose if they were going south of the border the chance of them been found are pretty low considering Bellick didn't find Surce that easily in season 2. I agree with you it seemed abit rushed, I was looking forward to the entire elaborate and clever escape plan that we saw from Michael in season one, especially since the prison was "air tight". Would have been more thrilling without the flash forward from the series finalie though.