1. this is the first board we make with the SAM3X but not the last one
we decided to adopt the mega layout to help people migrate their apps as easily as possible. In the future we'll explore different layouts.
2. The Due follows the R3 layout that we developed to make the standard layout more flexible/homogeneous (i.e. having easy access to the I2C) and to support boards operating at voltages other than 5v (IOREF PIN)
Unfortunately the mega328 on the UNO has I2c multiplexed on two analog pins while already on the mega (or leonardo) they are on different pins. Any current Arduino boards is based on R3 and solves the problem by placing I2C in the same position on every
As I just mentioned this is the first board with the SAM3X we're going to release so there is plenty of opportunities to create different layouts (as a matter of fact we have a new layout we've been playing with for a while)
I think there is a lot of people who prefer to re-use as much as possible of what they currently have before they have to throw everything away.. Our current Eth and Wifi shields, to mention two, work with the Due as they are able to detect and adapt to the whatever voltage the main board is operating at.
Making the board 5v tolerant would have made the it way too expensive. The market is now full of heavily subsidised (even sold at loss...) products that make it quite difficult to fight these battles.
The beauty of open source is that in a few days time you will be able to download the Arduino Due eagle file, design a much better layout and sell your own boards benefiting from our lack of vision
we introduced the R3 layout a long time ago and we explained why the IOREF pin is there... some people understood and implemented the correct measures to make their shields compatible, some others didn't ... you'll see a lot more shields made available with the full implementation of R3
Next week we release IDE v 1.5 and there will be a blog post discussing some of the internals of the new version.
I don't have specifics on that.. as I said there will be a blog post
1.5 will be Due only at the beginning. shortly after there will be a 1.0.2 with some of the enhancemens backported (there are some nice user experience improvements in it)
Later on when 1.5 is stable we'll merge and have only one IDE.
if you can point me to an issue here http://code.google.com/p/arduino/issues/list
I'll have it checked.