If you feel that strongly about the advanced editor, there's nothing forcing you to use it; the site does warn you that it's irreversible before you switch. It might have been a good idea to test it out on a new story instead of an existing one to see how you liked it. But if the popups are the main complaint, just close the ones you're not going to be writing in as you go? That's never something that's ever really registered with me as a difficulty in my own work, though of course they'll add up if you're just leaving them all open.