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The difference between a v-drive and direct-drive is the drive shaft itself. A v-drive is shaped like a V. The shaft goes from the motor to a transmission inside the boat and back toward the prop. A direct-drive has a straight shaft that goes from the engine out to the prop.
A direct-drive engine is located mid-boat, whereas v-drive boats have engines in the rear. Skiers like direct-drives because they have flat bottoms which create small wakes and handle well, but depending upon how the ballast tank of a ski boat is filled, a v-drive can maneuver a boat through the water, cutting the surface and creating a wakeboarder or skier's dream wake.
The difference is actually placement, orientation and extra equipment. Direct drives have engines mounted mid-ship and oriented with the output/transmission pointed aft, the shaft being driven directly from engine to prop. V-drives are mounted more aft, turned around so that the drive is pointed forward to a transmission and then to a transfer case that turns the power 180 degrees and down to the shaft, giving the "V". V drives, at least in larger boats, normally have a steeper shaft angle vs. direct drives because they are mounted further aft but have prop locations in the same place as direct drives.