You could try getting him up earlier to get him moving - maybe he'd be hungrier if he were a little more awake. The sugary cereal doesn't matter - he'll spike with energy and be hungry in an hour. Don't push it. You could switch to whole wheat waffles just to get a more complex carbohydrate into him.
My son LOVES my version of an "Egg McMuffin" - whole grain English muffin, toasted. Then I make an egg in a small pan - pour the egg in, and as it started to set, I throw a little cheese into the center, fold the edges toward the middle to make a little envelope, turn it once, and put it on the muffin. Wrap the muffin in foil and he can take it on the bus. You can also put a little turkey bacon on the muffin, or a slice of cheese on the muffin instead of in the egg. There's a lot of protein in it and the kids think it's fast food.
You could do a whole grain cereal bar too. Pack a snack with protein in it too.
Kids DO learn better with a decent breakfast in them, but you need to be more creative and stop feeling guilty - you're doing everything you can!
I also have a great receipe for protein-packed French toast and pancakes which my son devours. I make a batch up, freeze them, and pop out enough for a meal - he always thought it was frozen/instant food, and he ate it! Let me know if that would work and I'll give you the details.
Also consider non-typical breakfast foods - will he eat a slice of whole wheat pizza with veggies and cheese? Or even just cheese? It's still whole grain and protein. How about macaroni & cheese, but made with the whole grain pasta - Ronzoni even makes a "white" pasta that's made with whole grains but doesn't look brown. I've seen butternut squash pureed and mixed in with the cheese to look just as orange as the Kraft stuff. How about carrots dipped in hummus? Maybe if he thinks he's snacking, he'll eat?
Also find out what his friends are eating and see if there's anything there you can duplicate.
Good luck!