Pure & Simple serves warm waffles with fruit toppings, yogurt shakes, and fruit smoothies among other things. All are very good. P&S is a great place for a quick breakfast.
Pepper Market at CSR does serve breakfast. Maya Grill at CSR has a pretty good breakfast buffet with all the "normal" stuff and some specialty items. MG is very reasonably priced and convenient.
I'm not sure about the Flame Tree. We usually go to Rainforest Cafe when having breakfast at AK.