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For the most part, it seems like those who were hurt the most by Penguin did in fact deserve it. However, there are plenty of sites that had stopped doing shady stuff years ago and can't really do much about it. The disavow tool would be great for them - even if it only partly removed the penalty. I am sure many webmasters would love to be able to just disavow all but the links they know are NOT a problem just to get halfway back to where they were before, since it is pretty difficult to tell sometimes what the problem is.
And that is another big problem - Sometimes there is no good way to tell what is wrong. Since mistakes do happen and not everyone is intentionally trying to game the system, Google could really do a better job of explaining what the problems might be.
I have been working with one site in particular that has mountains of useful content, good site structure, nothing spammy on page (anymore - it was a little keyword heavy about 6 months ago), no paid links and not a significant number of keyword anchored links. Yet on Penguin day, the site dropped. We found and removed a few links that may have been a problem, but there were really only a few and they weren't glaringly obvious. Months later, reconsideration request replies still say "no manual action" and there has been only a slight recovery. Basically it is almost back to April 23rd rankings, despite the addition of lots of good content, a serious fine-tuning of on page technical stuff, and a decent number of genuine, good links - especially when compared to the competition. So it seems like there must be some kind of filter holding the site down, but no clue as to what is wrong.
It is frustrating for me as an SEO, but even more so for the client whose only "crime" was making a few rookie mistakes and got a little keyword-happy.
At this point, if I got a reply from Google that said "There is nothing wrong now, but we are penalizing you for the next 6 months/year/eternity..." I could accept that and at least I would not feel like I am in some parallel universe where good optimization and legit links mean nothing.
A life sentence because someone thought they would do a favor and put up a few exact match keyword site-wide blogroll links? Really?!
2 years, 6 months ago on The Dark Knight Rises: How Being Bruce Wayne is Not Enough to Save Gotham