Personally, I like it the way it is. I was not confused by the AREF at all, my problem was that initially I did not pay attention to the fact that the shield had wired the pots to 5 vdc. Then in my haste to compensate I over drove the A/Ds by attaching AREF to 5V. Through this I learned a lot about the Netduino and its relationship to the Arduino. I won't make the same mistake again and hope that my original post will help others.
I conform strongly to the concept of modularity, therefore I feel that if the shield uses A/Ds then it is responsible for supplying the AREF. It may not matter much in the case of a connected shield, but having the A/D source supply the AREF is one sure way of insuring that the A/D's are reading accurately.
So my vote would be, If you are going to add "internal AREF" it should be done via a jumper on the Netduino and the jumper should be left off by default.
I plan to make all my projects supply the AREF for accuracy, so don't break my projects please.
I literally only just discovered what the hell AREF is even for last night when I tried to work with analog inputs for the first time, but I totally agree. An internal AREF (as long as its controlled by a jumper) would be a nice convenience, but now that I sorta get what I'm doing, I'd rather not give up the bit of flexibility I only just discoverd I have.