Yes, I suspect the reason it is more smooth is because it has 2 cyl, while the 4 stroke has one.
The Tohatsu/Mercury/Nissan is not a bad motor, just not as refined as the Yamaha.
The Yamaha 4 stroke (2 cyl) is silky smooth, in the 6, 8, and 9.9 models. (note: I think we missed it, but I think there is a new Yamaha 6hp 1 cyl also).
They both weigh 55-60#, and the yamaha makes less noise (at least IMHO) since it does not need to run wide open to get to hull speed.Likely noisier???
What's the weight of the Yamaha?
Can you give me model number?