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Is the commute 2 miles or 20? Kind of makes a difference.
Fair point. When I had a semi-regular commute of ~35mi per day I did prefer using clipless, carry a change of top (+pants&socks if crazy rainy), maybe use a helmet, carry a bidon etc... but generally on my much shorter commutes (~12mi per day) I use flat pedals, no special gear except gloves and some things for rain stashed with locks in a pannier or saddlebag.
Is the commute 2 miles or 20? Kind of makes a difference. But yeah, breathable waterproof jacket, warm gloves, nice hat. Adjust to taste.