My views, when it comes down to it, it makes little difference about changing exercises, So i'd tend to agree with JB. Sure, Tim is correct that you will use more motor patterns, but will that lead to hypertophy? I dont think so. Obviously, a more efficient CNS leads to more hypertrophy potential, but changing the exercise and thus the motor patterns will basically put you back into newbie stage for that exercise, where your body basically just learns how to lift the weight as far as intramuscular co-ordination, motor unit synchronization, rate coding, proper reciprocal inhibition, etc. Thats why most studies on initial gains from weight lifting are neurological, after the neurological stuff happens where the body learns how to lift the weight, hypertrophy kicks in. Other studies show that the transfer rate between similar exercises, such as flat and incline bench, is pretty low, due to these reasons.
Now, im not saying stick with one and only one exercise per part, obviously things such as structural balance and what not have to be considered, but i think for the most part maximum hypertrophy per body part would pick the biggest compound exercise like a squat or a deadlift and focus on that lift and keep getting stronger. Obviously you will experience plateaus, but then i feel it'd be a better idea to change the paramaters of the exercise, such as the intensity, reps, etc... rather than the exercise itself. | 
