After lots of experimentation I have settled for thin, breathable shell (no insulation). I have a Patagonia jacket with underarm vents. Then I layer wool underneath depending on the temperature. I can put its hood under the helmet.

On the bottom I use Pearl Izumi bibs. Goretex hiking shoes, wool socks. Sometimes I'd use rain pants, but they don't breath too well. I tried SealSkinz socks, but they're way too warm for anything above freezing and below freezing there is no reason to wear them. Goretex shoes will usually keep my feet dry enough for at least 40-60 minutes.

Gloves are a problem still. All waterproof gloves I tried are too warm and too stiff. So I just use whatever gloves I have and let my hands get wet, which is usually not a huge deal for a short commute. Wearing latex gloves makes my palms sweat too much. If it's close to 32F (0C) and raining hard I won't ride anyway, due to the risk of wet ice, and that's the most miserable type of weather.