I'm in Ottawa, Canada and our winters are pretty damn cold (with the exception of this year so far) Here's what I've been doing since it started getting cold/messy.
I use Time ATACs with MTB shoes. I put my shoes on first, then I wrap my shoes with a plactic (grocery) bag. Then I put the neoprene bootie on. When I first started doing this, I would cut a hole out for the cleat, but later I realised that with the Time sysem, I could just clip in with the bag on. I can't speak for other systems, but it works great for me. The added wind protection is great and it keeps me dry in all conditions.