I used to ride year-round in New England, and I think this is the key concept to bear in mind.
Best system I found was neoprene booties over the shoe (essential if your feet might get wet in puddles or snow) with regular socks. Then you can layer old-school style with a thick wool sock *over* your shoe (cut a slit for the cleat), under the bootie.
You can also suck it up and try larger shoes just for winter, so those fancy warm-but-thick socks fit.
Some people seem to like neoprene socks, but they were awful for me. My feet got soaked with sweat and my toes froze like ten little popsicles.