All the way at the end of the API guy page, he makes this remark:
"With API literacy you don't have to understand how APIs work, but you should only use online services that have an API, and know who has access to your data and content, while also being able to download and walk away with your own valuable information that you have generated via ANY online service." This last part will not happen on its own. When data structures themselves are not in sync, we need again other APIs/middleware to export/import. It would also require to give the individual access/change rights and the right to be fully forgotten.
One big limitation I can think of is the propagation of errors.
I would say the subway system would be a fitting metaphor for now. Dark tunnels connecting various points in the information landscape. Traffic goes both ways, and those who can read/understand the plan can travel effortlessly and almost continuously between home, bank, local counsel, school, shop, etc.