I like this idea. Maybe a there's a limit to number of non hub/base departing/arriving flights based on reputation? I think you still need to have a hub/base to accurately base the aircraft to ensure that maintenance is done.
My thought would be this:
1. Based on reputation, you're granted a set number of slots which do not need to originate from a hub/base.(point-to-point)
2. The plane still has to be based out of a primary hub/base.
3. You a you can do a point-to-point from an airport served by a direct route from your base. Almost like a stopover flight.
For example:
My aircraft is based in Atlanta. I have a flight which goes from ATL > AUS (hub-and-spoke). I now have the ability to add a point-to-point from AUS > DEN. The flight would then work in reverse DEN > AUS > ATL.