Four days and two pages of discussion late to the party the weight and complexity of the trains barely touch the tip of the iceberg with the B&M Flyer trains.
A single car on one of the trains weighs as much as an entire train for Magnum XL-200. In high stress areas of the track the spine can get as thick as 4.5 feet due to the weight and the forces the train is pushing on the track. To top it off, the weight of the trains makes it incredibly stressful on any moving parts for the ride such as the lift motor, brakes, and drive tires.
Complexity wise, each train has locking mechanisms inside the harness that attach to the arm rests. Due to the already huge weight there's a buss bar that provides power to the train so that batteries aren't needed to lock and unlock the restraints. Not to mention there's the swing arms and the chassis mechanism that permits the train to swing and lock into the flying position. There's so many sensors in a single Flyer car that if one doesn't read things properly the ride will go down. Combine this with the trains communicating with the ride itself through an optic light connection, if it's not lined up quite right, if someone's too tall, hell if the sun's in the right place in the sky that day it could knock the ride out because the ride system has lost its method of communicating with the trains.
Operations wise Flyers are also a total pain in the ass to deal with in terms of guest safety. If their legs aren't secured in the leg flaps properly a rider can very easily break their leg during a ride. Evacuating riders off of a train is also a very laborious process with multiple steps involved, and requiring a hand crank for the chassis pins, a T-key for the harness pins, and a paint scraper for the redundancy pin to actually allow guests to get out of the seat in the flying position.
Costs are one factor in a lot of parks opting not to build one but the rider safety question is another one many people often don't realize.