Yes, I know that's the thing to do, but you must agree with me that it's something unnatural.
I have thousands of incoming links, and only exchanged or asked for less than 20 of those. The rest are natural. If I spend time analyzing links it would be something absolutely artificial.
The same goes with quality pages. Let's say that I have four or five pages that are the most referenced in my industry (just and example, of course). Visitors that read those pages get really good, top class information. But I have an Amazon datafeed in my site.
Suddenly, the information of those top quality pages are hidden from search results in Google because my site has an Amazon datafeed?
I know it's a simplistic example, but it can be translated as:
"A good article isn't good anymore just because of a site penalty"
It seems that Google is saying something like "Hey, you can't read this amazing article because it is from a site has lots of junk. So suck it up and read this article of a lesser quality but from from a pristine site!"
It is not about my site anymore, but about trying to understand the concept of it all. And of course it is an extreme example, but I think it is relevant.