Having owned both Yanmar engines and equipment, and Kubota engines when I had my rental business, I'll offer my opinion. You won't go wrong with either one. All things being equal, the Kubota is a better cold starter. The best Yanmar I had was in a first generation JD skid steer, when it was the same as a New Holland, but with a Yanmar engine. It was a 4 cylinder direct injected engine, which was uncommon at the time (around 1990). It was markedly more fuel effecient than its NH counterpart with the V1902 Kubota. Since it didn't have glow plugs, any idiot could start it in any weather. I also had a Yanmar built excavator which was very good, but by competitive standards, was weak and under powered.
One thing to keep in mind is that Yanmar's primary business is marine engines. The tractors, excavator, and engine sales are a sideline. Kubota's bread and butter is tractors and engine sales. And since they don't private labes for anyone AFAIK, they are solely responsible for the design and content of their product.
One thing to keep in mind is that Yanmar's primary business is marine engines. The tractors, excavator, and engine sales are a sideline. Kubota's bread and butter is tractors and engine sales. And since they don't private labes for anyone AFAIK, they are solely responsible for the design and content of their product.