I initially went with Pearjets, but quickly swapped all of them over to Aeroeagle: at least in my runs, they seem to generate more money even if I don't max out the plane.
This is because of the speed. More speed = more cost = less money.
I also use Aeroeagle as my only 2nd class planes because of this (and Kangaroo as 1st class planes). Is better to get more money, even if your trip is 15 minutes longer, because you won't always be there when the plane arrives.
It's true, and is a very wrong design problem. The games push you to get more airports (also, growing is the base of that kind of games), but if you have a lot of airports, you diversify the offer, so is more difficult to fill a plane. Nimblebit should be aware of this and find a way to fix it, because people won't continue playing for too long if they don't have the need of leveling and increase the number of airports.
Also, layovers are pointless. They need too much effort and money to bring the goods to the red airports, and you don't get more money. The difference of price between the layovers and the "original" goods of the final airport is because the difference of distance between the airport where the goods are to the ending destination and the distance of the "node" airport to the destination.
But, for example, if I'm in LA and I plan to bring some goods to Tokyo, if I layover goods to LA from other US cities, I'll loose money, because the layover goods to Tokyo will be cheaper (the cities are closer to Tokyo) than the ones that are from LA. Also, layover force you to play continously the game.