I have been keeping my mouth shut so far because I only use email for personal communication, and therefore do not have a very complicated Gmail set-up. This difficulty is a mere annoyance to me, but it is an annoyance.
I don't know if I read it in this discussion, or in another on the same topic, but someone suggested deleting Gmail from the Internet Accounts list, then adding it back. (There may have been a "close Mail" instruction in there somewhere.) I did it. It scared me at first, because it looked like the inbox wasn't going to rebuild, but I went to another folder then back to the inbox and it began to rebuild. Since then, Mail has sync'ed better with my iPad & my iPhone, but not consistently perfect as before Mavericks.
There are other annoyances. For example, there are too many Gmail folders in Mac folders instead of the clear distinction between the two groups of folders, and Gmail Spam shows up in Junk Mail but is not marked as junk so cannot be given a thumbs up if appropriate. I hope that the engineers have spotted these issues as well.