1) There is no option to say "reply using the same 'from' address that the mail was sent to." This means that you either have to set up an "identity" for every possible e-mail address you use, or you have to reveal your "main" identity to anyone who sends you an e-mail (and possibly confuse them in the process).
2) If you get new mail and read it on your iPhone or any other computer while thunderbird is open, then the status icon/indicator will get permanently stuck in "new mail" mode and you have to restart the app to get it to disappear.
On the plus side, the search is excellent.