As so often in motorsport, the V4 engine itself is not the 'holy grail' but the ability to package the modern MotoGP around it. A V4 Yamaha will be a completely new bike. There is nothing wrong with either power or power delivery of the inline 4. It's just that with the addition of ride height devices and aero the engine width does not allow it to be mounted as low in the bike as the narrower V4.
If you ever get to see in the engine bay of and F1 car, the V6 engine is a tiny jewel of a thing packaged very low and mostly hidden.