What Yamaha has done is create what's called a cross plane crank. A traditional four banger has what's called a flat crank. It has two rod journals at zero degrees and two rod journals at 180 degrees. The new Yamaha Crank has one at zero, 90, 180, and 270 degrees. This crank constantly has a piston producing torque on the crank. It not only solves problems with inertial torque, but also allows the engine to produce torque in a more consistent manner from combustion events.
So what's the downside of a cross-plane crank? Well, they tend to produce some wicked second-order vibrations. These can be cured with balance shafts or even isolated with cleverly designed engine mounts. However, right now they are only being employed on high-performance engines where it doesn't really matter. But if you've ever wondered why a Ferrari sounds like a like Ferrari, it's because they are using this technology in their V8s-but that's a whole different column.