Thidea is good. I'm sure many people (including me) have thought about this once .
The problem is that if you usually have several multi-part conversations you would have many more log files. And then, howto search for a log file? you look for a certain thing b@blah.com said and you can't remember when they said it, and with what other people in the conversation it was said, so you won't easily find it if multi-logs where grouped.
I think that although it's not the best way to store multiple-part conversations, it makes sense the way it works now.