Pierre Igot at Betalogue is frustrated 
by the not-very-smart algorithm that controls the way Mail threads messages. It doesn’t have to be as dumb as it is, he reckons:
As far as I know, Mail also uses unique e-mail message identifiers in the message headers to follow threads even when subject lines are changed. So it obviously can be smart in some cases. Why does it have to be so dumb in other cases?
He wishes that Mail had some kind of manual command to separate emails that Mail has mistakenly dumped together.
Kevin Bjorke, a Shading Engineer at NVIDIA, wonders why Mail.app won’t tell him what messages have been moved by its rules as Eudora does. “The program hides information from me and puts the burden of organization onto me to keep in my head — the opposite of what “productivity software” is supposed to do,” he says.
Rob Hyndman has just switched to Macs, buying a shiny new MacBook Pro. He is liking the whole experience , especially using Apple Mail:
Apple Mail is a joy to use on this box. Very simple, elegant, clean. I’m forgetting Outlook already :). But I do need to figure out proper archiving of emails. I have 5 years worth +, to about 5 gigs of email that I need to have handy and searchable.
One reason Mail can’t split threads is that threading is often performed by the IMAP server, not by Mail.
I’m almost certain Apple Mail totally ignores IMAP server threading and uses its own mysterious method of client threading. I’m currently basing that on crude examination of the Message framework with output from:
strings /System/Library/Frameworks/Message.framework/Versions/Current/MessageOne of my IMAP server supports:
THREAD=REFERENCES
THREAD=ORDEREDSUBJECT
… but neither of those strings show up in the Message framework output while many other IMAP capabilities can be found there.
One of these days I’ll enable Mail debugging and hopefully get a better understanding of the IMAP client/server interaction.