Many of the topics you raise have already been covered on Meta (browse the comments and comment-replies tags and this question's related questions). Comments are purposefully not threaded discussions to discourage their use: answers are the goal, and comments should only be used for minor remarks, corrections that don't warrant an edit or clarification requests.

If you want a more comfortable UI for comments, you can use a script:

• SE Modifications -- Username autocomplete in comments, inline revision source, and utility links
• "Reply" links on comments
• Threaded comments

If a user changes their name, the discussion thread might get difficult to follow, but if the thread is really that complicated, it may be time to clean up or wrap up. @name matters for notifications, but that's not an issue unless the user changed their name right before you posted your comment.

Involving other users, as in “perhaps @name could shed some light on this”, can be done on the chat. If the user participates in the chat associated to your site or tags, you'll be able to notify them that way. If they don't, it's their choice not to get involved. SE isn't a social networking site.

For linking to answers that already explain one subcase well, just use the link button below each answer. I often don't even include the author's name in that case: “Under circumstances A, use [½-line summary of method 1](link to other answer). Under circumstances B, use [½-line summary of method 2](link to other other answer). Under circumstances C, do <explanation of method no one has mentioned yet>.”

Many of the topics you raise have already been covered on Meta (browse the comments and comment-replies tags and this question's related questions). Comments are purposefully not threaded discussions to discourage their use: answers are the goal, and comments should only be used for minor remarks, corrections that don't warrant an edit or clarification requests.

If you want a more comfortable UI for comments, you can use a script:

• SE Modifications -- Username autocomplete in comments, inline revision source, and utility links
• "Reply" links on comments
• Threaded comments

If a user changes their name, the discussion thread might get difficult to follow, but if the thread is really that complicated, it may be time to clean up or wrap up. @name matters for notifications, but that's not an issue unless the user changed their name right before you posted your comment.

Involving other users, as in “perhaps @name could shed some light on this”, can be done on the chat. If the user participates in the chat associated to your site or tags, you'll be able to notify them that way. If they don't, it's their choice not to get involved. SE isn't a social networking site.

For linking to answers that already explain one subcase well, just use the link button below each answer. I often don't even include the author's name in that case: “Under circumstances A, use [½-line summary of method 1](link to other answer). Under circumstances B, use [½-line summary of method 2](link to other other answer). Under circumstances C, do <explanation of method no one has mentioned yet>.”