I love Thunderbird. I use Thunderbird. I want Thunderbird to survive and be successful. But I've never actually been able to make full use of things like flags, smart folders, or the built-in anti-spam because it's all local to a single computer. Those benefits don't follow me to my phone, or to a friend's house, or between my laptop and desktop.
We either need more extensions to IMAP (but what clients would support them?) or we need better web apps.