There seems to be so many. I'll start the discussion off with the problem I see and hear most - writer's reluctance to edit their works.
I've had many authors tell me that they chose to self-publish because they were afraid that a traditional publisher would edit or change their words. While this may be a possibility, it is definitely not a reason to withhold submissions. Your editor wants your book to be successful, s/he is not taking this opportunity to turn your idea into their own. Besides depending on your contract, you should have some say in the final product.