personal messenger app opinion:
all messengers, in one way or another, have to balance between security and usability.
for example, end-to-end encryption by its very definition makes it very hard to sync message histories between different sessions (say, desktop app vs mobile app).
not using phone number as user id will make it harder for people to find new users via their contact list, as will decentralizing the network.
it's all a trade-off, either in favor of security or user-friendliness.