I suspect it is in part because there are typically fewer top level comments than non-top level comments and all things being equal the best comment is likely to be a non-top level comment.
I think it is in part because, while good questions are good, good answers to good questions are better.
I think it is in part because a top level comment is more likely to be low quality. It is where spam is most likely. It is where users with less interest/skill at engaging others in discussion are more likely to post. It is where drive by comments will park. It is where generalized trolling will take place. It is where conspiracy theorists will show their tin foil.
Good luck.
