Dont really know of any bad kubota engines. But those are basically the same engines. Same bore/stroke. The 2.4 just adds an extra cylinder. But its all dependent on application. And which variation of the 1.8L and 2.4L.
But if you are that concerned about the engine.....try to go with the largest displacement for a given HP. The 2.4 is in 40hp tractors on the small end up to about 50HP. Then they throw a turbo on and push it up to 60hp.
So if you are looking for a 40HP engine.....The 1.8 is about maxed out. And the 2.4L is obviously barley breaking a sweat if it can handle 50% more power and a turbo.
I assume maybe you are looking at a 3560 vs a 4060?? If thats the case....dont get hung up on the engine. They are both good in the GL platform. But the 4060 is physically a larger tractor. Bigger tires, a little longer, few hundred pounds heavier. The 4 cylinder will run a little smoother naturally