I don't think this is the last revision of the due that we'll see. My guess is that something as tasty as in board Ethernet is too tasty to ignore, just like external memory banks. The critical issue here is backwards compatibility, ie the desire by the arduino team to maintain the mega form factor. IMO, it would have been better to start anew, with a square pcb format that better lends itself to lots of pin outs.
But I'm sure they have their reasons, it's their product, etc.