The 3-cylinders are quieter andsound more 'refined', while the 2-cylinder clank can give you a headache - and you really should use hearing protection with them. It all depends on how much tolerance you have for 'crude'.
However - the two cylinder tractors have an advantage that they are designed to be simpler and a lot easier to work on. For example, on my YM240 I can reach under the dash to replace the tach (or anything under there) in maybe 5 minutes tops. Maybe 5 minutes to pull the fuel tank. On later Yanmars these projects could take hours.
It's not just the number of cylinders, but also the design philosophy became more complex on later Yanmars. I think for tractors just entering their second thirty years, the older all-steel ones are going to be more maintainable.
But there's no strong advantage to either style.
Yes, you need considerably more cc's in a 3 cylinder before you match the torque of a 2-cylinder, for the lower half of the rpm range.
I wouldn't be surprised if there was more demand in Japan for the quieter 3-cylinder because of noise zoning. A lot of rice there is grown near residential areas. I wouldn't want to live next door to me!
