The Yamaha YZF-R1 is the first road motorcycle to use true MotoGP technology. The innovation it shares with Valentino Rossi's YZR-M1 centers around the engine's crankshaft – literally – and is, specifically, the orientation of crankpins along the crank and the firing order of the cylinders, governing the interval between each firing.
On a standard inline four, the two outer pistons are up (top dead center) while the center pistons are down (bottom dead center). If you looked end-on at the crank, the crankpins (the pins joining con-rods to crank) would be north and south. As the crank spins the two pairs always stay 180 degree opposed to each other. The firing order – the order in which each piston has a combustion stroke – is, typically, first piston, second, fourth, then third. The interval between each bang is evenly spaced – four bangs the same time (and degree – 180 degree – of crank rotation) apart.
The cross-plane crank Yamaha YZF-R1 still has four cylinders in a line but the crankpins are evenly spaced around the crank ever 90 degree – if the first is at top dead center, or north, the second and third are east and west, with the last south. The order in which they fire is 1-3-2-4, and the interval between each firing is staggered, it's irregular, rather than the regular firing of a normal inline four (in fact the inline four Yamaha YZF-R1 and YZR-M1 MotoGP fire with the same interval as Honda's VFR800).
Power isn't everything, utile the 2009 Yamaha YZF-R1 all modern 1000cc inline fours had 180 degree, regular-firing configurations because the alternatives didn't offer big advantages. Historically, big displacement sports engines needed lots of power, alternatives made less power because they needed beefing up to cope with vibration, and second, smoothness, for ergonomics and reliability. Developing 180 degree inline fours offered more performance gains than pursuing new designs. Yamaha explored the crossplane crank in the 70's but didn't pursue it for the reasons above.
These days the challenge isn't more power – 1000cc sportbikes make 160bhp, which is plenty – it's making it more accessible. Electronics are one solution; use traction control so all the pilot has to do is be an on/off switch – pin it and let electronics take over. But Yamaha don't believe these are the only solutions. Having paved the way for full traction control on the road with fly-by-wire throttle control on YZF-R1 and YZF-R6s, they've also looked for mechanical ways to improve the relationship between the rider's throttle input and grip at the back wheel. And they'd already found it, in 2004 on Valentino Rossi's MotoGP Yamaha YZR-M1.