Sorry if I get out in left field here, but I must plead ignorance on Independance Air. Some observations, that is all:

1. Since there is no FC seating, I wouldn't go for a revenue-based model. I think that pax would be flying here because the fares were better than what they could get elsewhere. If the fares were on the level of the majors, then I think most FF'ers would buy a ticket on them, hoping for extra miles, upgrades, etc. So, I'd say consider segments.
2. Have one elite level and offer it pre-boarding.
3. Have preassigned seats.
4. Don't lie to us.
5. Make decisions quickly. If there's a problem, know when "to fold 'em" versus trying to fix it or wait for conditions to clear until past midnight, when there is NO possibility of getting to your hotel until after 1 am with no chance of getting a meal.
6. Probably not practical, but in relation to #5, could we have free hotels even if it is weather-related? (I know, probably not, as margins are thin already, but just a thought)

Best of luck!