My biggest annoyances:
* Inability to easily edit the from address
-Why: I use Fastmail with 10 different custom domains and custom senders. In TB I would have to manually add in each sending domain. And TB still doesn't "remember" which -from- addresses are used by which -to- address. This used to be solved by the https://www.absorb.it/virtual-id/ . Shockingly, the Fastmail webui does have this feature.
* Inability to minimize to tray on Linux (Windows does have this feature, but that doesn't help me).
* Inconsistent notifications, sometimes you'll get one, sometimes not, who knows why.
* No easy way to tell if Thunderbird is using IMAP Push
But at least I'm glad they put an IRC client in. If there's one thing I always wanted my email client to be, it's an IRC client. (sarcasm)