One thisng I did not mention that I like about a seperate hood is that it moves with my head and does not block my periferal vision.
I use the hood on my storm shell only when the wind is biting, and end up having to push it out of my eyes all the time.
For around $20 you can get a very good performance fleese hood/mask that will last years.
The biggest problem is that they can be too warm. Though with temps below 20* for the last few weeks, that has not been a big problem.