The biggest reason for it is that in practice email isn't as open and decentralized as people like to think. For most of its history all advancements were controlled by Microsoft, AOL and Yahoo, and today it is controlled by Microsoft and Google.
Most of the OP list of things they don't like are about client UI presentation. Inherently unrelated to the protocol itself.
I don't have any of those issues because I use a client that does the interaction and presentation exactly how I like it.
Reformatting top-quoted replies. This is possible with email because you can pipe the messages through any preprocessing you want. Inserting custom processing into the delivery pipeline is generally impossible with all proprietary systems, but easy with an open standard like email.
HTML formatting: Again, easy due to customizable preprocessing and/or viewers.
Eighty people responding to a thread: This is threading, handled natively by most good email clients. Gmail makes a mess of it though, so I get why it'd be painful if you use gmail. Don't use gmail.
> because the protocol leaves so many decisions up to clients.
I feel like this is a misunderstanding. The clients have nothing to do with the protocol (SMTP), that's the job of the MTAs (mail transport agents).
The client provides the UI/UX interaction part. It is an immense strength of standards like email that there are tons of clients. You may want a completely different UX with your email than me, so you're free to have it exactly the way you want and so am I. And we can still message each other. This is impossible with proprietary walled gardens.
Email threading is trivial, nothing magical about it. Most every decent email client will properly thread conversations. Gmail will not, so yes gmail is super painful for long threads. Use a better client.