Email sucks less than any other communications protocol.
The quote from the author is exactly correct. Users hate email because they use broken clients, like Gmail. Using a real client like mutt (https://lwn.net/Articles/837960/) is a pleasure; for one thing, it threads conversations correctly, unlike Gmail and almost everything else.
I used mutt, thunderbird, apple mail, outlook, gmail, sogo, roundcube and they pretty much all have the same issues. Yes, some make use of Thread-id a bit better than other (I like the way apple mail show thread and thunderbird is "okay", although sometimes it handle edge case in a weird way), but overall, they cannot fix fundamental flaws in the format in itself:
Emails are hard to search, the threading model is simple but quickly turn into a graph with many leaf which become a mess to properly show and follow along, again, a lot of emails are outright broken and then it is up to the client to try to show what it can, the dates should not include timezone which is dumb so everybody do it anyway but follow their own standard, so you are not sure your client will correctly parse the date, files are encoded in base64 for hell-sake, ...
I'm currently touching the plan 9 email tools a lot, and recently rewrote the acme mail client. There are warts, of course, but the ones you've discussing are either related to the underlying communication and not the format, or are easy to deal with.
I'm not sure why you say emails are hard to search. Extract the text and put it into an engine like lucene. There are the usual small corpus problems, but these aren't dependent on format.
As threads are fundamentally a graph, so complaining that the structure matches the structure of the data is... Odd.. to me.
Including the time zone in the date is a small wart. Add an extra specifier to the format string and move on. Base64 is similar: a bit annoying, but decode and move on. And use RFC1652.
> Yes, some make use of Thread-id a bit better than other
Traditional email threading was based on the contents of the In-Reply-To and References headers. The algorithm is described in RFC 5256 for the IMAP SORT and THREAD extensions[1] and used in several mail user agents[2].
