This season I have been using the booties that fit over your clipless shoes. They rise up past my ankle and are windproof, but not waterproof. Surprisingly though, I have worn them in the rain and they kept my feet pretty dry regardless. I have seen a vast improvement in my comfort using the booties and not had to change my pedals or my shoes.
Last year was a struggle to keep my feet warm. I think this year is going to be much better.