Some good thoughts, and a lot of us are thinking along the same lines it seems.
On a practical and not particularly costly level, the two things I think that would show appreciation of "Frequent Flyers" would be:
- A "Fast Track" line at security when things are busy (thinking of the "maze" queue in BNE for example)
- A priority boarding lane at the gate (a la "Priority AAccess") to allow "anytime boarding".

On another note, anyone venture a guess as to what "Next Generation Check-in" will hold? An RFID card as they where taking about perhaps?