If we look around on the Internet we can find many stories about the new Yamaha triple-cylinder engine that powers the 2014 Yamaha MT-09 motorcycle. Some of this stories are pretty good and some are not really based on any truth. So what configuration did Yamaha select for the 2014 Yamaha MT-03 triple-cylinder engine?
First, each cylinder in a four-stroke engine can be fired in one of two ways, depending on which downward stroke of the 720-degree cycle is used as the intake stroke that begins the cycle for that cylinder. In any engine with a given configuration, this gives the number of possible firing order as 2n, where n is the number of cylinders.
As you found, this gives eight combinations for a three-cylinder engine with evenly spaced crank throws. However, half of those combinations are duplicates with the entire order 360 degrees - one full revolution - out of phase. This reduces the number of options for the Yamaha MT-09's three-cylinder engine to four. Of those four firing orders, three are essentially identical with the big-bang configuration you found of all three cylinders firing with 120-degree spacing, followed by a long interval of no firing. Note that all three have a 1-2-3 order. The remaining configuration is the even spacing of 240 degrees between each cylinder's firing, with a 1-3-2 order.
In practice, this gives two options for a three-cylinder engine with evenly spaced crank throws: 1-3-2, which gives the even firing order, or one of the three 1-2-3 big-bang configurations. Yamaha uses the 1-3-2 even firing order, as does Triumph for the Daytona 675 and MV Agusta for its F3 models.
According to Yamaha, the crossplane concept as used in the three-cylinder engine provides linear torque development in response to the rider's throttle input; while the even firing intervals ';provide smooth torque characteristics and a good feeling of power in the low- to mid- rpm rang.'
Note that the crossplane crankshaft of the Yamaha YZF-R1, which has its journals evenly spaced at 90 degrees, cannot have a similarly even firing order. The options for the Yamaha YZF-R1 are either all four cylinders fire in sequence 90 degrees apart or the uneven order of 270-180-90-180 that Yamaha eventually chose for the latest Yamaha YZF-R1. Only on engines with an odd number of cylinders is it possible to have the combination of evenly spaced crankshaft throws and an even firing order.