Original poster stated, "... it'd be kind of a shame to finally get there with 1990's cryptography."
The RSA encryption algorithm has been around a lot longer than the 1990s. In fact, it was released in 1977. Still, the technology and algorithm continue to work. However, due to advances in computing and hardware, the encryption keys have had to be extended. So, there is nothing wrong with the older technology.
When my brother and I started a business in 1994 to provide a secure communications platform for the masses, RSA and the related PKI infrastructure were all the rage. At that time, we had DES and Triple DES - AES didn't exist and the legal status of PGP was up in the air. RSA Laboratories had a great licensing deal for BSafe and TIPEM that made it possible for a small startup to develop some really cool products without breaking the bank. But, we soon discovered we were up against both Microsoft and Netscape who were releasing secure email solutions. And, the gov't sponsored Clipper chip was at the forefront. There was a lot of uncertainty in the secure communications market back then.
Despite our product being built from the ground up to provide encryption, digital signatures, anti-spam, secure file transfer and secure FAX facilities in an easy to use package (initially for Windows 3.1 and Mac System 7), we ultimately felt we couldn't compete with FREE and never released our product.
While we set out to make PKI a manageable process (no easy feat), the biggest barriers were trying to convince the general public why it was important to protect one's privacy and why people should want to pay for our commercial product (to be sold in CompUSA's everywhere!). We shut down our business in 1996 having never gotten the product to market.
GPG and Enigmail provided the privacy and authentication features while still being bound to existing and clunky client mail agents. However, the web of trust never really took off and the PKI infrastructure is a real bear. I don't know how many people use the tool with private keyrings vs the WOT.
On the Anti-Spam from, Yahoo! developed DKIM which relied on digital signatures. Sadly, it has limitations and isn't the end-all-be-all cure for spam it was hoped to be. I still believe a product, developed from the ground up with privacy and authentication in mind and not a bolt on to another system could solve a lot of our woes. And, I am sure that brilliant folks could probably come up with a way to anonymize the traffic so that it metadata analysis would be nearly, if not entirely, impossible.