There are of course some red eye flights.
In your example of MIA-LAX the flight is about 5 hours. I would say the downtime is about 30-45 minutes at LAX and you can get the plane back to MIA.
The trick is what time you want the flight to leave the first city. If you assign a flight at 9am you may have missed the business rush. As a business flyer I need to get out at 6:30am or 7am to make a meeting, etc. At the same time, I want to head back around 2-3pm, and not 5-6pm.
If in the game you have a flight that leaves at noon from MIA-LAX, it could in theory make it back to Miami at Midnight or 1am. Not sure how many passengers would fly.
Lastly, your ticket prices have to reflect peak times as they do in real life. I think the easiest way is to have player set a price (MIA-LAX $400) and then the AI makes subtle changes based on demand, your flight schedule takeoff time, etc. You would also need to account for travel agent discounts, and in later years internet discounts.
Auto connect would work IF there is a flight at the hub destination at a particular time...
DEN - MIA #1
LAX - MIA #2
Two flights heading for Miami. They both land in Dallas.
There's a DFW - LGA flight #3. It leaves at 10am.
That means #3 is leaving at a non-peak operating time, so less Dallas to New York passengers. BUT, it may be picking up some passengers from the Flights #1 and #2 that are connecting there to New York.
Flights #1 and #2 would need to leave early in order to be in DF by at least 9:30. It is a 3-3.5 hour flight from LAX. Which means you have to have Flight #2 depart at 6am or 6:30am... great for business travelers but not likely the same as a peak time of 8-10am.
For Flight #1 it would need to leave around 7-7:30am to make the connecting flight.
In an automated world, IF your passengers don't get there they have to camp overnight for tomorrow's flight. Not good PR.
This is where an airline sim will differ from Cities in Motion 2 (I play that too
) because that game is made up of a smaller scale area with lots and lots of travel patterns including just walking... trams, trains and buses. These options would not be available in an airline sim. You only have whatever planes and flights so have.