Could it be that we are operating with a paradigm that is antiquated? As much as Penguin is supposedly about link profiles and anchor text, could it be that other factors are used to determine if a site qualifies for a penguin penalty? For instance.....
Anchor text vs. brand name. What determines if people are using your brand for an anchor text? Could it be whether or not people search for your brand name alone or in conjunction with an article they are looking for? If so, then you are becoming or have become a brand.
Amount of links vs. amount of traffic and traffic patterns. If you have 10k links pointing to a site but only 1k people per month, does that look a little strange? If those 1000 people bounce like rubber balls yet the site is linked to all over the place does that look a little fishy? Or if they do not stay to read, read other pages, or there is not any user activity on your site beyond the occasional ad click or sale, but there are bucket loads of links pointed to the site, something is wrong.
Do a little test. Take the top positions in the serps, look at their user metrics, and then ask yourself the question. Based on this information alone, do they deserve to be where they are at? If they have a lower bounce rate, higher time on site, and higher pages viewed per visitor than you do, whether you like it or not, they deserve to be above you.