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Some people suggest that this is exactly what should happen.
Interesting idea but there are so many barriers to it being possible to implement. Multiple depots? Shared depots? Who pays for what?
I guess where the analogy falls down is that trains are a necessary public service in a way that air connections are not. Therefore you need someone to run services on routes that aren't profitable, and to work out how to incentivise them to do that.
There are equivalent in the airline world, look up Public Service Obligation routes. These are subsidised routes that mean some regional airports are connected to the national hubs where no alternative public transport exists with a journey time of under 3 hours.
Some people suggest that this is exactly what should happen. The model would be the same as airlines where (as I understand it) airlines bid for departure slots and it's then on them to make their service as competitive as possible to attract custom and make profit. The claim is that what you end up with is a price war and better and better deals for customers.
I guess where the analogy falls down is that trains are a necessary public service in a way that air connections are not. Therefore you need someone to run services on routes that aren't profitable, and to work out how to incentivise them to do that.