Subsidies

[Zortan]

I also think that if a certain country has little to no service than the airline subsidiary should receive some kind of bonus like a higher than normal starting reputation, or reduced gate fees or something.

No but why? If someone wants to start a business in a challenging environment, let them - there's no reason to help them out. However increased starting reputation (or whatever measure of how well-known the airline is is implemented after the reputation system gets changed) should be somehow proportional to the reputation of the parent airline.

EAS in the USA, and PSO in the EU...
But generally, you are correct.