Leverage Independence Air's unique position at Dulles Airport to make its frequent flyers real VIPs at Dulles.
Redemption opportunities could be for free parking, especially valet parking... or airport limo services... free drinks onboard... will Independence Air continue to operate its lounge? Redeem for memberships.
Parking would be a benefit to leisure travelers, since business travelers expense it. But parking could be an elite benefit for business travelers if it meant they had access to valet, drop off the car and go.
Definitely offer an elite level program. Priority checkin, priority security, and priority boarding. Consider a companion pass like Southwest. All elites get lounge access.
If the airline is considering something that's directly revenue-based (I think it could rub some folks the wrong way, but let's go with it) why not take it to its logical conclusion. Why not offer cash rebates instead of redemption? So I buy a $500 ticket and get 3% cash back. Granted the marketing tie-ins are revenue generators, so losing that would be a drawback if you see a Starbucks partnership as an independent money maker rather than a cost.
Another elite benefit would be waiving change fees and (if they exist) standy fees. Also allow same-day confirmed changes at no cost.
Similarly a redemption opportunity would be to use FF credits to pay these charges.
Whatever you do, twelve-month expiring points are a very very bad thing. Don't do it. Don't do it. Don't do it.