A few thoughts on direct toots/direct messaging:
Direct toot notifications get mixed in with faves/boosts/mentions. There are the toggles in the web UI but they are a little hard to find, and take something like 3 clicks to pare down the notifications. I’d like a separate icon, maybe with a little notification dot, to see direct conversations – single click.
Ideally the API would also provide a separate hook, so apps can implement a similar UI change.
I noticed while exploring a little on the GNUSocial side of things, postActiv has some form of direct messaging implemented (not clear if they ever finished implementing federation for it, maybe someone in the know can clarify). I don’t know what their implementation is, but it seems like it would be smart to work with them to maximize interoperability.
If Mastodon did that, direct toots could remain as-is - just another privacy level of toots, with the actual direct messaging in another part of the interface.