Jeff:
I like your idea about the e-mail. I'll go one further. How about allowing "standby" for miles upgrades. They could timestamp the list and when seats are made available, you'd get them automatically.
David' point about checking F seat availability before booking is a strong one. I always check the number of F seats using www.itn.com before booking a flight. If I'm flexible in travel plans, I try and book the flight with the most F seats.
I've found this most useful on EWR-IAH segments which are always a tough upgrade.