I would never have taken the show this direction. Instead I would have stayed true to tradition: Guns, Robots and uber-awesome fight/chase sequences. I would have continued to elaborate on Derek's memories of the future. I also would have continued the odd chemistry between John and Cameron, and continued to develop Cameron as she learns more about humanity and it's ethics/morals. I would never have over-developed background/guest characters that didn't have to do with the future of mankind like this show has(especially dead-end characters like school prom or whatever).
I wouldn't ever do any of those music-video sequences. I might still have introduced Reily, but I would have revealed her true identity MUCH sooner instead of letting people hate her for so long beforehand.
This is not a thread to just ditz on the things you don't like, but a place to explain what you would do differently.