Or maybe use high speed trains for the shorter distances, freeing up more space for long distance flights.

To be honest it wouldn't be a problem to have airports far away from city centres if they are really fast trains to the city centre. But in London for instance, all express trains to airports are express only in name.

While not really that fast, I used to love Heathrow Express when you could check your luggage at Paddington and step on knowing you didn't need to deal with checking your luggage at Heathrow.