Breakfast in Madison Wisconsin
Marigold Kitchen is exactly the kind of place you describe. It's half a block from the square around the state capitol. This is not a fancy place; it's more of a coffeehouse atmosphere - walk in, get in line, give your order at the counter, and they'll bring it out to you when it's ready. They have rotating specials; last time I was there, in fall, they were serving pumpkin pancakes. They can get a bit busy but the line moves quickly. Best breakfast in town! www.marigoldkitchen.com
Another possibility is Sardine, maybe half a mile from the square, an upscale bistro in an older renovated warehouse type building facing the lake. They serve a very creative brunch on Saturdays and Sundays. If it's a nice day, you can be served al fresco out on their deck overlooking the lake, the most spectacular view over Lake Monona you will ever see!! It's just lovely, and the food is excellent. www.sardinemadison.com
Both serve their special brunch menu on Saturdays; check out their brunch menus on their websites and you'll see their unusual offerings. I've had breakfast/brunch at both of these places, and both offer the creative menu items you are seeking, not just your standard breakfast fare.
You can find more discussions about places to eat in Madison in these topics, but they are not specifically about breakfast: