Slack supports shift+CRLF for line breaks, so users can write epic poems broken up in to hundreds of stanzas if they want to. Using Slack as a one-line-at-a-time chat service is a choice that a user makes. Slack itself doesn't enforce it.
Topics are all jumbled together in a channel so it’s nearly impossible to piece together the full conversation.
Only if users interrupt the current conversation with something else. Again, this is a cultural choice that users make. It's not a Slack thing, or even a chat thing. Also, Slack does support threaded conversations (albeit with a pretty horrible UI).
Important team knowledge — like what decision did we make and why? — gets buried and lost within hours (even with powerful search).
I totally agree. Slack is not the right place for documenting important stuff. Nor is a different chat app, or email. Important knowledge should be put in a knowledge management app (eg a repo wiki for code, or a Word doc for business related things).