Good points.
I have an issue with this:
"The internet should have been made to be anonymous and encrypted from the get go, so that all information should have been hidden from snooping 3rd parties by default"
Right now, the deep web & dark web has that if you choose. One could argue that effectively centralizing the security in a single protocol may make it more vulnerable to exploit compared to the random/heterogeneous 2nd party solutions. Perhaps it would merely add another layer of security though...
If all security has vulnerabilities, is it more secure to lock something twice?
Is it desirable to create something so secure that all criminals below state level actors are removed from competing in the crime game?
If you think of security like an antibiotic, how do you use it to cultivate a desirable biome of microbes?
What are the properties of a beneficial vs a malignant biome?
Yes that is the debate focus point between layer 1 anonymity and layer 2 anonymity.
Since TCP/IP is very hard to change, if a major vulnerablity would have been found since it's implementation like MD5 which was a standard hashing algo back then turns out to be rubbish by now.
That would have been a crucial failure if we'd have to swap the entire internet right now.
However if there is no anonymity by default then you always go back into the hamster on a wheel problem.
Most people are ignorant, they don't know why privacy is good for them, and they can't possibly concieve how the lack of privacy will come back to them in forms of identity theft, real theft, and other kinds of bad things that come from knowing too much about somebody.
So the debate is between security vs privacy.
You either have something very simple as core layer with no privacy, just basic stuff to keep it simple and secure.
Or you have full privacy built in it, and then you risk the algorithms becoming weak later once some flaw is discovered.
This is the debate between BTC and Monero as well. I'd personally like the Monero concept better, if enough research would go into making sure the enryption is solid and flaweless.