Sophia's is like that girlfriend you broke up with last month. You know the one that you can't stand but keep going back to because the sex is so great? That's Sophia's: great food, questionable execution. The bakery items are bar none and the ever-changing menu is filled with all sorts of organic breakfast goodness.
However, the dining room is tiny. No waiting area to speak of (unless you count the sidewalk) and only four tables. You often will have to share your table with one of your fellow Madisionians. This can either be an interesting way to start your Sunday morning or really, really awkward. Also, the hours are hinky. Only open weekend mornings and even then, Sophia's closes randomly.
Despite all of this, it's worth it. Sophia's is a hidden Madison gem that shouldn't be overlooked.