I use the fan myself. I've never used the flywheel, but I'm interested in what others have to say, because I don't understand the principle behind the flywheel.
I've used both for the past 3 years. I don't think the flywheel is there to provide resistance, but to give a better road feel-which it does. The fan is definitely there to give resistance! When it's all the way open, I can get my HR up into zone 5z if I want to.