One of them being complexity and and how fast you can move on new features. Adding features to a spec'd standard is a horribly slow process, this is the reason the developer of Signal decided against decentralization. You end up building XMPP, and that doesn't go so well if your specs are not very explicit. You can see this in how unreliable OMEMO is with multiple resources connected.
The Web is already a mature platform and has not actually made things more interoperable. It replaced a lot of the previous internet infrastructure that was (IRC, Newsgroups, SMTP which still somewhat clings to life)
> Adding features to a spec'd standard is a horribly slow process
It doesn't have to be. The Web evolves relatively rapidly these days, and Matrix does too (although it could be faster, for sure). It's important to support freedom as well as privacy - as per https://matrix.org/blog/2020/01/02/on-privacy-versus-freedom.
The Web is already a mature platform and has not actually made things more interoperable. It replaced a lot of the previous internet infrastructure that was (IRC, Newsgroups, SMTP which still somewhat clings to life)