There are a couple of not-so-obvious reasons to like Boma and Kona Cafe.
The juice.
The coffee.
Both have specialty juice drinks that I love. Boma has "Frunch", and Kona has "Lilikoi". Both have tropical fruit juices blended together, so it's a nice departure from typical juice you get anywhere.
Both places have press pot coffeemakers, so you're not getting the infamous "Nescrapé" coffee. I didn't come up with that. It's one of those terms that the people on the Restaurant board came up with.
With the press pots, you're getting "real" coffee. Good stuff.
All things considered most of the other breakfasts at WDW are pretty much your standard fare. You'll find eggs, maybe a frittata omelet, the breakfast meats, sausage gravy w/biscuits, fresh fruit, lox and bagels, pancakes and Mickey waffles, and specialty breakfast pastries. Oh, and the cereal and oatmeal areas, too. Every place seems to have something else that stands out, like a breakfast bread pudding or something wacky like that.
My recent favorite "outside the box" breakfast item I had in October was a roasted tomato with a lightly sprinkled melted parmesan on it. That was at Captain's Grill (formerly Yacht Club Galley).
My advice with Fresh and other places that make made-to-order dishes like omelets: Try to gauge the ebb and flow of the line for the omelets. It seems that there are slower times to get your order in, and other times when it's mobbed. Sometimes it's better to wait and then you won't have long to wait for one.
Its fun when the park is almost empty. The characters are also cool! 
