Comments are impermanent. They've always been meant to be. The problem is, unless a moderator goes through a question and physically deletes the comments, they're pretty permanent.
Why is this a problem?
Comments distract from their parent post. Often, comments contain information that is better suited to be in the post itself, or better suited to take place somewhere where extended discussion is welcome.
Comments are almost always a point in time blurb. They don't have the edit history of a post, and they don't flow logically as a post might. They are purposefully unstructured.
In short, comments are weeds that grow up around the useful questions and answers, and because it is impossible to prune them sanely through any human means, they proliferate, and cause a user to have to read not only the answer, but all of its comments, and attempt to parse out the relevant points from the non-relevant ones.
Yet, by default they are permanent, insofar as they remain around unless deleted by a moderator (or flagged often enough that they're deleted by the Community user)
This should change.
Comments are meant to ask for clarification, or to address points that are meta to the post itself: whether it should be closed, re-opened, or deleted.
Once that clarification is received, it's always better to put it somewhere where it will be seen by a googler: into the relevant post (either the question or the answer the comment seeks clarification on).
Comments should be auto-deleted after a period of time (a year is a good starting point for discussion), and this should be communicated to those that leave comments in a non-obtrusive way. This non-obtrusive message should be shown to the user the first time they leave a comment.
Part and parcel to this is an appropriate merging of the third place with a post. If people want to chat about a question, the third place should automatically set up a link to the question so that people can chat there. I recommend a 'chat' link right next to the 'edit' link for users that have the ability to chat.
If you disagree with this feature request, then please share posts where a comment was left years ago that is relevant and useful now, but shouldn't be 1) its own answer, 2) its own question, 3) an edit to an existing answer or 4) an edit to an existing question.
This related question talks about a user being able to set an expiration date on comments. Another older feature request asks for very much the same thing. I'm not asking for such complexity. All I'm asking for is that all comments are deleted after 1 year.
Please note: This feature request is primarily for Stack Overflow. We see thousands of new posts a day, with the potential for tens of thousands of comments a day. There is no level of flagging that could even come close to dealing with the number of irrelevant comments lying around. Even if there were enough flagging, there aren't nearly enough moderators to deal with the resulting flags.