Web browsers could bundle everything with the next update or use the one already installed, see tor browser bundle for example. No need to educate users. Other software could rely on preinstalled daemons and guide users to "install the internet" on first use if necessary.
And ISPs shouldn't be able to do any harm with those transport nodes, they shouldn't be able to even see what kind of stuff those nodes proxy.
How is this any better than IPv6? Each browser having its own overlay sounds like the good old days of AOL.
Ignoring that massive issue, which daemons get installed? Who installs them? Who updates them? End users won't. So it's up to the Software+OS vendor and ISP - Just like IPv6.
Don't get me wrong, IPv6 has been, so far, a pretty epic failure in terms of adoption. But your plan seems to put it all in the hands of the exact same people, but at the same time, gives them a massive incentive to partition the internet into a whole bunch of tiny walled gardens.
And ISPs shouldn't be able to do any harm with those transport nodes, they shouldn't be able to even see what kind of stuff those nodes proxy.