That is like saying V-6 or V-8, which gives more horsepower if all other variables are equal?
Yes bigger is better in this example....but, like all rules, there is an exception.
A 2 stage 5.7" vac motor might have 100cfm and 105" of water lift and pull 9amps on start up.
A 3 stage 5.7" vac motor might have the same 100cfm, but be rated at 130" of water lift and 11amps on start up.
Since both are plumbed in "air-parallel" in your example, you would have Double the cfm (200) and the Same waterlift as a SINGLE vac motor. 200cfm and 130" lift is nothing to sneeze at, and 200cfm and 105" is still very effective on shorter hose runs, especially if the hose is larger, like 2" truckmount hose.
Besides the obvious "size" issue (a 3 stage is taller) you have Amperage issues to contend with, there might be a reason a particular manufacturer used a small and lower amp draw vac in a particular set up.