Your Thunderbird experience is almost completely opposite of mine. Gnus is my main e-mail client but there are a couple of Windows machines I run Thunderbird on.
All of your points can be solved by going through the configuration options. Maybe that shouldn't be necessary, but not everyone's the same.
Likewise. There hasn't been a lot of innovation in the Thunderbird client, but it consistently and mostly stays out of the way. Search is pretty fast and messages go where they're supposed to go.
In ~five years of using it across three machines, I've only had two instances in which a folder got corrupted, and in both cases I was able to repair it and recover the messages.
Also, when I migrated from Windows to Linux, transitioning my email profile was utterly seamless.
All of your points can be solved by going through the configuration options. Maybe that shouldn't be necessary, but not everyone's the same.