Well I love whole grain sourdough, but while I don't have a starter going I'm okay with making regular whole grain yeast bread. But only if it has risen enough. I do three rises, and the time depends on the temperature, but normally it is 4 hours for the 1st, 2 hours for the 2nd, and 1 hour for the final rise after shaping and before baking. So it's a total of 7 hours-it's definately gotten broken down some by then, and it also releases more nutrients that way.
I also like to experiment with sprouted grain occasionally. Sourdough is best, but this is an okay compromise in my book. This coming from someone who is not anti-grain though.