You're adding things not in the OP list I was responding to so I didn't claim that. But let's try:
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.
