I am considering embedding the Due in an existing system where +5V is readily available.
The Power section of http://arduino.cc/en/Main/ArduinoBoardDue
Supplying voltage via the 5V or 3.3V pins bypasses the regulator, and can damage your board. We don't advise it. This appears to be true for the 3.3V input.
However, I see no downside to powering the board through the 5V input on the 'Power Header'. This seems identical to what is being done already by supplying power from the "USB Programming Port".
One exception, may be that it's unlikely reverse-polarity may be applied via the USB jack, and there is no specific reverse-polarity protection on the 5V line.
There is also the issue of connecting the USB for programming and having two 5V supplies connected through T2. However, this would also happen if power was supplied through the DC Jack 'X2' (which I believe is typically A Bad Idea). Matter of fact, I don't see how T2 does anything useful at all.
Perhaps I'll remove F2 if I go this route (Isolating the 5V from the USB programming port).
For an illustrative alternative to the power section of the schematic, look at the PDF attachment here:http://arduino.cc/forum/index.php/topic,146574.0.html
(that I keep updated), or a static version attached below.
Am I missing something? Any suggestions/observations welcome.