One problem is that if you're replying to a message, and
save the reply as a draft, then finish and send the draft later, the 'answered' flag doesn't get set on the original message.

This is a real drag for me, as I save skeleton replies as drafts, and flesh them out and send them later (so I can reply to them as they come in); but when I look at my mailbox, I'm missing the 'answered' flags that tell me which messages I've responded to and which ones I haven't.

I wonder if this is a limitation in the asynchronous manner in which I compose and send replies, or if it's a bug in mail.app (and works properly in other mail applications).