Bear in mind that three-seasons shoes are designed to keep your feet cool. So you're working against the shoe's design when you try to keep your feet warm.
The other thing to consider is that it's blood flow that distributes heat. Tight-fitting three-seasons shoes can reduce blood flow. Cram in thicker socks, and something's gotta give--usually blood vessels.
For a cold weather shoe, whatever your final choice, make it a metric size or two larger than your three-seasons shoes so that you can get warm blood where it needs to be, while at the same time adding insulation.
I strongly prefer clipless. My choice is the Lake MXZ series of clipless winter cycling boots. I have the older MXZ302 model.
The current model is the MXZ303, which seems to have addressed my only two issues with the 302s.
These are a full-grain leather boot that's fully insulated. They are waterproof. I can stand in an ankle-deep puddle without water getting inside.
The cleat backing plate is embedded within the sole, on the outside of the sole's insulation. This avoids the heat-sink effect. Besides insulation in the sole, they come with insulated insoles. They're flat, so if like me you need arch supports, they go in right on top without issue.
They are also durable. I'm beginning my eighth winter with mine. This mitigates their expense a bit, althought theyr'e still breathtakingly expensive.
At the beginning of every season, as you would with any leather boot, I give them a new coat of waterproofing. I use Kiwi's Wet Pruf, found in the shoe polish aisle of the grocery store. (Trouble is, every year I forget I still have some, and buy a new tin.)