>By design as in, that's the only way the network could conceivably work.
This network, yes. But you can construct truly anonymous cryptocurrencies with e.g. zero-knowledge proofs, yet the author(s) chose not to. This would have enabled AP, maybe answering PGs question in point #2 of his post (https://news.ycombinator.com/item?id=5547423).
I didn't know the original code was that buggy, I confess I was lulled a bit by the line "This was the only major security flaw found and exploited in Bitcoin's history" in the wiki article. Maybe it needs changing in the light of https://en.bitcoin.it/wiki/Common_Vulnerabilities_and_Exposu... :-)