Last year I rode in my regular shoes with Defeet Woolie Boolie socks. I have the old version of Performance Bike's neoprene bootie. Has a heavy duty zipper and heavy rubber sole. They're the most durable shoe cover I've owned. In fact, they're the only shoe cover I've own where the zipper hasn't broken and the sole torn to shreds over the course of a season. The problem is they're bulky, heavy, and the thick neoprene fits tightly around the ankle so it limits movement. It's a trade-off for keeping my ankles warm. The new version is neoprene all around and lacks the rubber sole. Lighter, less bulky, but not as durable and prone to slippage if you have to put your foot down since there is no tread.
This year, I got smart and covered the vents on my shoes with duct tape on the inside. That with the wool socks has been fine on my commutes (under 30 minutes) down to 20F. I'll be adding a different windproof shoe cover to add a little warmth. On longer rides (read: snow) or below 20F I'll have to go back to the heavy neoprene covers again. When it gets down around 0F and lower, I add chemical warmers.