OK, I really, really miss having one view in which I can see all my unread mail from all my accounts in one place.
I’d also like to be able to configure it so that when I’ve closed the hierarchical view for an account, selecting the account name shows me the inbox instead of that page full of options. Those things are all irrelevant to me anyway; that’s what the toolbar and menus are for. This would make my sidebar more usable, since as it is now, I have to scroll it to get to all my accounts.
It can take a while for Thunderbird to come back up after I click it in the Dock after having closed the main window. Interestingly, it doesn’t always happen, just sometimes.
One moderately nitpicky thing: the little box you click to choose which columns are visible in the message list window doesn’t exactly stand out. I hunted for about 20 minutes to figure out a way to remove the “thread” column, since I prefer not to view as threads anyway.