In my case I believe it was too many exact match anchors and not enough generic click here and raw URL links.
So yes I agree with you, I have some good examples, for example I have 2 sites in the camping niche - one site serves one product size and the other the larger size.
I built links to the smaller size product - using exact match anchors, on the other site I never got round to the any link building, the smaller product site with the exact anchors got the beating and the other site was left alone.
I have another example, two sites selling the same product - one to the US market and the other to the UK market, both sites are unique content affiliate sites. I did the exact match anchor link building on the US site - the UK site I left alone as it was already ranking highly, and again the site I built exact match anchors to took the beating, the UK site I left alone is still ranking.
So for me it was exact match anchors, perhaps google have also weaved some on page stuff into the mix but I am not seeing it in my case.
I am reading about Penguin been based on a self learning algorithm but I think that is giving them too much credit. I am seeing anchor match penalties and no recoveries are happening because that is just how the algorithm is setup - you get slapped and stay slapped - at least for now.