So far as I can tell, the Founder had no interest at all in organizations of any kind.
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.