Both are good engines. I have a Yanmar Main and a Kobota Genset. My Yanmar (3HM25F) needed to have double pulleys made and installed to drive a small frame 124 A alternator. It is not recommended to put a large frame Alternator or to run a small frame with a single pulley because it will damage the water pump bearings. I don't how the alt belts in a universal are configured.
Another concern to address is maintenance accessibility. My Yanmar oil change is through the dipstick on the stbd. side. Mt engine access is from the port side so I have to climb over the engine to make an oil change, My Kabota has access and drain plug on the stbd. side so it is much easier. These are a couple of things you might consider.
The Beta someone mentioned is set up for easy maintenance, so you might want to take a look at that one.
Another thing to look at would be the cooling system. The fresh water cooled Yanmar has an integral heat exchanger properly sized for the engine and I don't know about the Universal. I personally prefer an engine with a separate heat exchanger, because they are easier to remove and clean, or replace plugged tubes, or exchange with larger if you prefer.
Sometimes an engine will overheat through impeller, belt, Blocked intakes, plugged mixing elbow, stuck thermostat, or other problems; and sometimes after that it overheats easier. Some of this may be caused by a film on the inside of the engine from the overheated coolant, and cleaning the engine doesn't always work as advertised. So when something like this happens it is great to be able to simply put in a larger heat exchanger.
None of these things I mention would disqualify any engine to me but would be little things I would look at.
Good luck
Joe S