That makes no sense at all. Arguments are meaningless because they are used too much? Utterly illogical, have I misunderstood something here?

Maybe I didn't make my point very clearly, and you're right, as stated that's not really what I mean.

What I was trying to get at is that topical debates where one side disagrees with the scientific consensus typically degenerate rather quickly into complaints about the scientific establishment itself, and about how its barely-permeable idea membrane has a tendency to shut down a lot of criticism without fully addressing it.

And this is a valid point; unfortunately, it doesn't tell us anything at all about whatever specific claim is at hand, it just tells us that science puts up some pretty strong barriers to new ideas. Which, I might add, is the main reason that science continues to work, because for every scientific theory out there, even the ones with the most solid evidence, there are dozens of vocal lunatics that have their own pet theories that "aren't being taken seriously" or "have been silenced". In most scientific fields, apart from a few edge cases where data is weak or theory is spotty, there usually is a very strong consensus on most issues, and they're settled well enough that criticisms will usually be dismissed out of hand unless there's a very strong reason to take them seriously.

That doesn't mean that if someone is being "silenced" or shouted down they're necessarily wrong, but it does mean that they won't score any points by complaining about it. That treatment is leveled equally on all new ideas, and even in the best case scenario it usually takes new ideas (if correct) a generation or so to make their way through the barrier (mostly because the new generation thrives on tearing down as many ideas from the old generation as it can, whereas the old generation fights to preserve the status quo).

A big part of the problem is both sides assuming the other is disingenuous.

I absolutely 100% agree. Whenever someone shouts "Fraud!" in these arguments, I cringe, because it's rare that someone will spend a lot of time and effort pursuing scientific ideas that they actually think are wrong.

FWIW, I'm not taking any stand on AGW here, I really don't know enough about it to comment intelligently on the science. But the argument surrounding it, politicized as it's become, has a very similar tone to the arguments about evolution, right down to many of the same meta-critiques about the scientific process. Those talking points were not helpful when applied to evolution, so I'd rather they fell out of the lexicon, their presence in an argument immediately rings several alarm bells due to the similarities. The similar argument style would typically make me assume that the deniers/skeptics are just wrong (if it walks like a duck and talks like a duck...), though in this case I'm reserving judgment because a few of their other points seem like they might have some merit.

Not being convinced is always valid unless there is concrete irrefutable proof.

Hmm, I suspect a lot of Less Wrong-ers would disagree with you there, the entire philosophy of that site is based around the idea (one that I find very defensible) that we should usually be thinking statistically instead of right/wrong, and even if we can't know something for sure in the face of uncertainty, any pair of people that are thinking rationally and honestly should, in time, be able to at least agree on likelihood ratios between different possible outcomes by recursing through all the relevant priors and settling discrepancies that way. "Agree to disagree" is merely a way of cutting off that recursive settling of priors, and will sometimes have to happen in the interest of having finite length discussions, but the goal should always be to avoid that, or at the very least, pin down the lowest level disagreement about prior probabilities so that we at least know that both sides have updated their beliefs based on the same evidence.

For instance, if someone was honestly arguing that special relativity was wrong with an X% probability, that's not valid at all unless and until they can go through the various evidences in favor of it (which scientists claim puts its likelihood of being right at, say, 99.9% (we really should be talking likelihood ratios, not percentages, but you get the point)) and justify a set of priors that would lead to that X% probability. Similarly, scientists should be able to go through the evidences against special relativity and and justify granting them less authority, by showing their priors. Then we can look into those lower level assumptions, and do the same thing. Obviously this process can balloon, which is why scientists hate to do this kind of thing when they could be doing real work instead. :)