The four stroke's displacement classes in AMA pro racing were chosen to make the four strokes competitive out of the gate in the late '90s. Four stroke motorcycle tech has improved greatly since then. The 450s make much more power than 250 two strokes and the same is true of the 250 four strokes and 125 two strokes. The manufacturers who call the shots for the AMA felt that four strokes were the future due to expected emissions laws, even though Honda for one had low emissions two strokes that raced in Dakar and Baja, and then sold 250 dual purpose low emissions two strokes in the rest of the world. They wanted the fields to be full of the new four strokes not old two strokes.
Two strokes need roughly a square bore/stroke ratio for best flow from the ports. Too short a stroke and the ports are just too small. Look at the cylinder of a recent two stroke road race bike and you'll see a forest of transfers, seven or more. Where as four strokes with valves in the head don't need cylinder wall area for flow so the stroke can be super short. Saw two strokes have short strokes for packaging, and they are industrial engines with small ports so they don't need the wall area.