Apparently Jesse was supposed to die after just a couple of episodes in season 1 but they thought he was too great of a character to just throw away.
The original story for the 9th episode of Season 1 had Jesse dying. Thankfully that season was cut short to only 7 episodes because of the writer's strike. Vince Gilligan decided that the chemistry between Walter and Jesse was too good to ruin, and adjusted the storyline for the upcoming Season 2 to keep him around.
Also, Hector Salamanca (old guy with the bell on his wheelchair) was originally supposed to be the "main" bad guy in Seasons 3 and 4, but Giancarlo Esposito (actor who played Gustavo Fring) negotiated his contract status to full-time, so again Gilligan tweaked the story to make Fring the main antagonist to Walter.
FYI - this is "technically" the last season, but not really. The season is split in two. There will be 8 episodes in 2012, then a break, and finally the last 8 in 2013. I prefer to think of them as two separate seasons, just so I believe this isn't the last one...
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