They started out on a particular design with a reasonable displacement that suited the times, like the BMW 500cc flat twin ... the R50/2 being the smoothest of all.
Then BMW, to "keep up with the Joneses" went to 600 and 750 and 800 and 1000 and 1200 cc, with the same engine layout, and the newer ones are nowhere near as smooth.
Norton. Started at 500cc, then 600cc, and then the 750 Atlas was almost unrideable due to vibration, which they fixed with the Isolastic system, but the early ones are a pleasure to ride with no rubber prostheses.
BSA. The 500cc models are noticeably smoother than the 650s. Never ridden a 750 twin, but I suspect that at high revs, the handlebars get to being 2" in diameter.
Guzzi - The V-twin started in '66-'67 at 700 - smooth as silk. Then 750, then 850, then 1000, then 1100, then 1200, then 1400cc. Even on a configuration with "perfect primary balance" like a 90 deg V-twin, it's too much ....