My commute is only 8 minutes and it is quite flat so I don't bother with the cycling shorts. If I want to wear heels that day, I just put them in my bag and I have a pair of cycling keens that I can use to clip in (which is kind of funny to do while wearing jeans). But sometimes if it's a more casual shoe choice that day, I will just wear the shoes and ditch the cycling footwear.

I have not tried commuting in a skirt yet, though I have with a 'skort' this summer. I definitely got whistled/honked at that time.