I've been using Thunderbird for a couple of weeks now, and I mostly like it a lot. Themes are great, extensions are great, integrated spam filtering is great (and it's good filtering, too). It's fast and stable and has a rich feature set. Switching over was easy. But there are a few minor annoyances:
There's no single-step way to empty your spam mailbox. You can select all and delete, or you can delete-all-spam and then empty the trash. I want a button on the toolbar that empties the spam folder. Why isn't there already an extension for this?
Sorting on a new field undoes the existing sort. So sorts on binary fields like read/unread show messages within the groupings in whatever order the messages happen to be in that mailbox, which might be rather random if I've been moving mail between mailboxes. You can move all your mail to another mailbox, sort in the secondary order, and move it back, but that's beyond cumbersome.
There's no compose-in-main-window. OK, that one would take more than an extension to fix, but I miss it.
I keep having to remind myself that even though I could write an extension to fix them, I Should Not Take On New Projects Right Now.