I read somewhere that the writers originally intended for only two seasons of the show. The ratings for the show were so good, though, Fox told them to stretch it out to keep it going. If you go back and watch some of season 2 I think you can see writing that supports this as they started killing off characters willy-nilly.
The show isn't as strong now but it's still appointment TV for me. Great concept, pretty good execution throughout. I'll miss it. T-Bag (especially during the first three seasons) remains one of the best characters in TV history.
p.s. - What ever happened to that Prison Break "Cherry Hill" spinoff?? The one with the women's prison?
I realize when you make a show like Smallville, you sometimes have to skip over the source material to make it appeal to the masses. This episode went beyond that, they basically took a dump on the source material and lit it on fire.