I once heard it said - can't quite remember when and where, unfortunately - that while all characters are different sides of the writer, the protagonist is naturally the most representative - you are your protagonist, basically. And it may take a while for the protagonist to come into focus and be specific and interesting simply because it's harder to see yourself. I recently finished the rough draft of a pilot, and while the protagonist is interesting, my writer's group tells me he doesn't "pop" as much as the two antagonists. And I must confess they were more fun to write - partly because they're so awful. But I'm trying to have faith that as I keep digging more as you prescribe, I'll be able to bring the protagonist up to their level.

I agree with this. It's a little weird when your first readers tell you how well defined the characters are... except for the protag. But... he/she IS the best protag for this story, trust me! The reason why it's obvious to us is because we write from that personal perspective but forgetting that what is clear to us may not be so to the reader. Giving the protag something that's not part of us at all helps to have a more objective look and better define their actions. It's a constant inside-outside back-and-forth search in order to get them just right.