> I wonder why the people responsible for making the design decisions for
> the final X1000 motherboard design ignored Paul's advice to stay away from
> the PA6T and look at using one of the QorIQ chips instead?

It's easy to understand if you look a the timeline:

- Early 2008: A-Eon's decision for the PA6T is made by the OS4 developers (as requested by A-Eon)
- Early 2009: actual development of Nemo board commences at Varisys
- April 2010: Paul Gentle of Varisys discourages from using the PA6T for new designs
- Mid-2010: Paul Gentle of Varisys recommends QorIQ

If you then add to this that the first somewhat suitable QorIQ CPU (P4080) started sampling in August 2009, your question should be answered in full.

You can find more information (e.g. on the viable CPU options besides PA6T back then), links and Trevor's confirmation there:
https://morph.zone/modules/newbb_plus/viewtopic.php?forum=3&topic_id=7348&start=85

> Perhaps the only reason was because using one of the QorIQ chips would have meant
> giving up PCIe lanes

While the matter of PCIe lane quantity is a valid one, I believe the reasons stated above outweigh it by far.

> and also meant further delays in completing the X1000 project.

At least delays in commencing, as with QorIQ instead of PA6T, the actual board development would have started at least 6 to 12 months later than it had with the PA6T. And this with a slower CPU (per core), no AltiVec and less PCIe lanes. Whether QorIQ would have meant less problems during the design process, I don't know.