Michaeluna,
From going over the DUE schematic some time ago, I remember questioning the existence of T2. It is a P-channel fet that always seems to be turned on. It doesn't harm anything I suppose. However, it would never turn off unless the 5V power port suddenly became negative. I've seen uses like this for battery-polarity reversal protection. I'm not sure how it applies here though.
I had some other minor comments that can be found here:
http://forum.arduino.cc/index.php?topic=146574.msg1101238#msg1101238
Also, when it is obvious, I think that judicious use of power-ports and net-labels make a schematic easier to read, and preferable over crossing wires (i.e. the bank of switches, digital pots, and so forth). If you're trying to convey special pcb grouping, routing, or operation with the display of the wires on the schematic, then a few words on the schematic print would go a long way to explain your intentions.
Rob is right-on about the junction dots.
Best of luck with your project.
Chris