This is pretty much my experience. The site is read-only for a lot of people. I think I was rejected the other day because I didn't have the 50 reputation to comment on a reply that had other comments on an older question. They need to lessen restrictions that got too strict out of fear of the site becoming worthless. Right now the scales aren't balanced.
Comments on SE are meant to be temporary( in their value, not duration ). If you had to raise an important issue about something, you should have instead asked a question about it, where you could leave a link to the problematic answer/question and explain the problem. In fact that is the usual procedure in case of conflicts. There is no restriction on that. If your point is valid, the community does the rest.
And yet frequently asking a new question seeking clarification on an old questions topic matter, due to some relevant restriction, or even simply 'this no longer applies to V2 of lib$foo' is met with cries of "duplicate" and buried. Stack Overflow is suffering from the Wikipedia Moderation Problem ... which a few of my friends now refer to as "using a mod_assholes reverse proxy"
Most comments should end up as an edit to the question or answer, clarifying some point, at which point they can be removed. The Question and Answer are the important things on Stack Overflow, not the communication that went into creating and tuning them.
The remaining comments are just fluff, such as "thanks", which can more appropriately (for the site) be expressed as an upvote or accept. Or they're asking a new question, in which case the parent's comment applies.
Interesting how this is the case, because that was one of the key goals of the site when they were first building it.
I listened to Joel and Jeff talk about it in their early podcasts when they were first building the site. To be the definitive answer for a question requires that the answer be able to change and evolve over time as new information becomes available.
