I do like the idea the Nodes giving power/Construction Hut aura, so the defense is actually feasible.
As for the proposed changes, they seem helpful and fine. Maybe the walls at nodes are a bit too much, don't think it's gonna be that useful and may look out of place. I would rather go for the route of captured Nodes giving worthwhile benefits.
Now this is a lot of content. I gotta take some time to read it all. Perhaps some ideas can be used, since there isnt enough people/resources to such a big Expansion anyways.
Some nice ideas. I generally like the possible changes to Willzapper/Fleshbender, that could affect transforming/transformed units.
Perhaps they could provide global buffs, as to make Transformation more interesting.