Some of the best handling bikes in the world have V-4 engine configurations. The MotoGP bikes from Honda, Ducati, and Suzuki all feature V-4 engines. That being the case, there must not be much of a disadvantage to this design from a handling perspective.
(although Yamaha, an inline 4 design, did take the 2008 championship)
One advantage is reduced moment of inertia of the engine. Even if the center of mass and mass were the same between an inline and a V, the moment would be lower on a V because the mass is closer to its center. In addition, with the rear bank closer to the center of mass of the bike and only two cylinders out front, a V configuration probably contributes less to the overall bike moment of inertia. That might be enough to counteract its potentially higher cg. Of course, this entire discussion is pure conjecture without comparing actual engines and bikes. Depending on how each is mounted, a V-4 could actually have a lower cg than an inline.The design limits options. It sounds like it has some advantage, but for the life of me I don't know what it is.
For ducati it was a natural move. They couldn't spin the twin fast enough, they can keep more of their proven design by going to a V, instead of starting from scratch with an inline.
I was under the impression that honda ran a 5 cylinder, and no idea on the suzi.
I would really like to know what the advantage of a V is. The disadvantages are clear to me.