I was told a couple of years ago by two very knowledgeable people that rel-canonical was a stronger signal than a 301, but that just doesn't make sense to me. A 301 is a clear signal that a search engine pretty much has to follow: the page is gone and has been permanently replaced. Rel-canonical is a suggestion, albeit a "strong" suggestion. The non-canonical page remains accessible, and for user-agents other than search engine spiders, there's really no indication at all that you're not looking at the official version of the page. But you may need to use rel-canonical because you want those filter pages to still be available to users.
I expect they'd eventually remove noindex pages (but not pages blocked via robots.txt if they're already indexed), but I figure it can't hurt to push it through.
Regarding the increase in the number of duplicates, are these the same URLs with more added, or a whole new group? It may be that by removing some dupes, they've been able to crawl a little deeper, giving them the opportunity to find more problems.
Edited by qwerty, 24 September 2013 - 05:47 AM.