Not flat, but staggered. They were flat before 09. A staggered crossplane crankshaft locates each connecting rod 90° from the one before it. According to Yamaha, this arrangement allows for the high RPM power of an inline-four with the steady powerband of a twin-cylinder bike.
The unique shape of the crossplane crank smoothes out fluctuations in inertial crankshaft torque to provide very linear power delivery as the engine's combustion torque builds, giving the rider more linear throttle response with awesome power and traction exiting corners.