> I am not sure what caused the design delays, or what mistakes were made, if any

I think one of the biggest pre-2010 changes in the X1000/Nemo design was the scrapping of several dedicated I/O chips in favour of the SB600 southbridge chip:

"the prototype Nemo motherboard development took much longer that originally estimated and much of the delay can be attributed to a change to the original design specification by the inclusion of an SB600 Southbridge, which although a technically superior solution, created several additional challenges in the manufacture and testing process."
http://safir.amigaos.se/main.php?d=newsfull&news=1133

"We had some difficulties with the getting life signs out of the SB600 (South Bridge)"
http://obligement.free.fr/articles_traduction/itwgentle_en.php

"The customer chose a PC motherboard South Bridge to handle the peripherals, and presented us with the challenge of getting it working within a PowerPC architecture CPU."
http://www.amigans.net/modules/xforum/viewtopic.php?post_id=51602#forumpost51602

"The SB600 doesn't follow normal PCIe address decoding rules, as in its original use as an AMD south bridge it was designed to appear as if it were integrated into the north bridge."
https://lists.ozlabs.org/pipermail/linuxppc-dev/2016-June/144114.html

The 2010+ delays that followed were more delays on top of that.


Edit: added another quote

[ Edited by Andreas_Wolf 03.08.2016 - 01:18 ]