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I've spent far too long staring at flight tracking sites, and occasionally I think I'll notice some pattern in what types of aircraft a given airline uses for certain scenarios/routes.

For example, Delta seems to operate a lot of MD-88's on short-haul routes that other airlines would likely use ERJs or CRJs on. They also seem to use 757s on quite short hops (ATL to southeastern cities ~1hr away).

Another example would be why British Airways operates 747s to some cities, and 777s to others, and exactly how they decide where to use which aircraft.

Is there a good reference for figuring out the reasoning behind why airlines use a given aircraft for a given route? Or are there too many different factors and too much corporate secrecy to really know for sure?

There are many factors, but you can often predict what class of plane will be used for a particular route by the distance and demand.

For smaller cities, they want to fill the planes, but they also need several flights per day to cover the fixed costs of serving that airport (and make things convenient for customers), so it's often better to have a commuter jet bouncing to the nearest hub and back several times per day day than one large plane that carries an entire day's worth of passengers in one shot. For larger non-hub cities, they'll do roughly the same thing but with mid-size planes.

Between hubs, they'll run the largest narrow-bodies to connect all the various small cities not served by a common hubs, plus hubs themselves tend to be large cities with plenty of native demand too.

For international, they'll run wide-bodies because they need higher fuel capacity, and there's rarely a convenient time for customers due to the long flight times combined with crossing several time zones, so you might as well pack them into as few planes as possible.

Notably, some carriers fly several different types, each optimized for specific route types, while others fly just a few types (or even just one) because that makes maintenance, pilot training and fleet scheduling easier--but may limit what kinds of routes they can fly profitably. When airlines merge, they'll usually have similar fleets--and in cases where they don't, they'll quickly start dumping types they don't like and replacing them with types they do.

Every airline has their own recipe and priorities in this regard and it’s unlikely you will find any open accessible references to this.

Apart from the obvious demand, availability and costs of aircraft and business they do take in consideration the wear and tear (and maintenance cycles) of the aircraft (how long to go before what maintenance) as well as a balance of long and short haul operations and the specifics of each particular aircraft and its parts. An aircraft with some inoperative equipment might still be legal and dispatched for a short haul flight but not ETOPs operations.

It can go down to small details like customer profile and preferences as well as configuration of the aircrafts interior (eg. newly upgraded seats) and the availability of service and maintenance facilities.

You also get the occasional really big planes on routes that wouldn't seem to necessarily make sense for the distance. This can happen when there's a big out and back that brings the plane back to the hub with some "downtime". For example, out of SFO, a large plane may fly a 8 hour leg out to a far point, and then come back. Adding time in for servicing etc, the plane would arrive back at the hub site around 18 hours after it left. It could serve the same route and just sit on the ground for 6 hours waiting, but why not send it back and forth to DEN for example, which it could do in that downtime. Or maybe the timing works to have the plane go to the east coast and then do a long trip out of there.