1. Spam false positives. I get order confirmations or mail list subscriptions sent to spam folder occasionally.
2. Search is really bad. by default it only searches subjects, and I think only in the current folder.
Thinking about moving to gmail, provided those guys sort out privacy issues.
1. Just add addresses to your address book to whitelist. Also make sure you use Report Spam/Report non-spam on enough emails (200 of each) to activate your personal bayes db (see the Options -> Spam/Virus Protection near the bottom to see how many of each you've already learned)
2. At the moment, you do have to explicitly add body: to a term to do a body search. The first time might be slow as it indexes your email, after that it should be faster.
http://wiki.fastmail.fm/index.php?title=NewInterface#Enhance...