I have an '06 Heritage which I upgraded to stage one, day one. I recently purchased an '08 Deluxe for the wife, which she requested remain stock. The Heritage gained horse power, but lost a considerable amount of low end torque doing stage one. Given the way the wifes '08 pipes sound, and the low end torque produced by the motor stock, I'm reluctant to ever do stage one to her bike. That being said, when I open the throttle on my bike, it will out accelerate her bike any day! I like to cruise, not race. I would prefer a good "sounding" Harley without sacraficing low end torque.
Did lose a few mpg but gained a much better running bike. It was really lean from the factory, white ashy looking plugs. So not only is it running better I would think it is much better for the longevity of the motor.
Not to sure what I was getting before changing over, but afterwards, with factory SE2 slip ons and a stage 1 intake, could get 50 mpg on highway at 55 to 60 mph. And as stated before, very noticeable power increase.