Possibly the problem with the 'Over-Due' delay is the result of a problem identified in the book 'The Mythical Man-month' (or some such title like that), where the more people you throw at a project the more time it take to complete it. Paul working alone might just have had too large an advantage?
That is known as Brooks Law (Fred Brooks wrote the MMM book). Here is the wikipedia entry on MMM http://en.wikipedia.org/wiki/The_Mythical_Man-Month
. However, Brooks Law would only come into effect if they added more people.
I have no knowledge of the Arduino team, but I have worked in the high tech industry for 33 years now, and I have seen many late projects. I suspect the second system effect in Mythical Man-Month may be more of the cause: The second-system effect proposes that, when an architect designs a second system, it is the most dangerous system he will ever design, because he will tend to incorporate all of the additions he originated but did not add (due to inherent time constraints) to the first system. Thus, when embarking upon a second system, an engineer should be mindful that he is susceptible to over-engineering it.
If not the second system, I suspect part of the issue is just the fact that DUE is a completely different system than AVR. Do you do things like map the Arduino pins to ARM, or do you force users to have various #ifdef's in thier code. I haven't looked at the details of either ARM or AVR chips, but it may be some things like interrupts, PWM, sizes of the 'int' type, inline assembly, etc. are completely different.