The security thing is the big one. No one should be putting their nsec directly into a bunch of different clients.
If you're writing for browsers you need to support at least NIP-07 for note signing. Mobile and desktop need NIP-46 for secure signing. NIP-46 itself depends on NIP-04 and/or NIP-44 for encryption.
Major clients don't use note IDs, they use bech32 identifiers. Those are defined in NIP-19.
Replies and common indexed tag types are in yet another NIP.
Then there's the outbox model, which isn't really defined anywhere at all, but is essential for a client to work with a distributed set of relays. That's pure institutional knowledge.
I agree with all of this except the need for nip46. Thats a nice to have, but not essential.
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What is the alternative on desktop or mobile apps?
There isnt an alternative. NIP46 shifts the signing and in essence that public key becomes a secret for that interchange, or a combination pubkey and secret. A security abstraction layer that can be chained.
