Are you sure? Howabout the single complement Kisshomaru ever got from his father (by lore)--on the founding of the Tokyo dojo? I think he wanted the organization to spread aikido, he just didn't want to have to run it.
In general, I do like having a parent organization. I like it that Hombu has decided to be an umbrella organization so I can walk into most dojos and even if they've never heard of my teacher or the ASU, they accept me because I'm affiliated with Hombu. I'd like to believe there's some quality control, so the more squirrely groups are easier to identify. It's hard to put a price tag on that.
I think that he liked the shiny new building.
He may or may not have appreciated the benefits of what Kisshomaru was doing (that story certainly suggests it), but that doesn't mean that he had any interest in the organization itself.
His massive lack of interest in organizations at any level has been mentioned by many of the uchi-deshi.
That's why I'm saying that calling it "the Founder's organization" is probably less accurate than calling it "Kisshomaru's organization".