I don’t give a shit about the “protocol”. I give a shit about the end experience: the system, not a single component of it. (The fact that you’re so narrowly defining the range of critique is very telling and noted, incidentally.)
I’ve given Matrix three tries now. Three times Element has shit its pants, lost all my keys, refused to recognize the backups I made using its own tools, and made me start over from scratch. It’s a fucking shit system, no matter how good or bad its “protocol” is.
Come back when you’ve got a product that doesn’t suck so hard it can suck bowling balls through garden hoses. (Well, no, don’t come back. Matrix is on the permanent shitpile for me along with Emacs, Haskell, Internet Explorer and other such software fiascos of epic proportions.) But start pitching the product when you’ve got a product that isn’t a festering pustule that periodically pops and spreads its grotesque fluids all over the place, not now when it’s like a rusty chainsaw made without a kickback guard.
One of the first things that you’d need to do to make the system not suck matter out of galactic core black holes is to look over the “Fallacies of Distributed Computing” and make sure that you didn’t interpret it as an instruction manual instead of a warning against them.