The site I am working on is relatively strong and has good ranks except for its homepage. My job, or nightmare if you want to call it, is to take care of all the duplicate meta description tags. About 8% of this site's meta description tags are exact duplicates of what their homepage uses. Considering the size of the site, we are talking about 200 pages I have to modify or delete if its thin content. Could the large number of duplicate meta tags be the reason why the homepage does not rank? Also the owner's WMT account only reports 2 duplicate meta descriptions for the homepage when I found almost 200 on indexed pages. Why Google lowballs the count in WMT I do not know.
The site did receive an unnatural link warning over six months ago. I got to see the report and Google noted they took action against those links instead of the site as a whole. As vague as this is, the owner claims he did not do anything wrong. A possibility is below.
The site's homepage gets copied by a lot of people. On average the owner is submitting 3-5 DMCA takedown notices each week. They are not just copying text, but the whole page (logo, pictures, sidebars, even the copyright notice at the bottom of the page, etc.). This is unnatural in my eyes, but may or may not be what Google sees as unnatural. Not that it is a big concern for the owner since Google claimed they took action against just the links and not the site.
I would not say the homepage is over optimized at 2-4% for its main keywords. Other pages on the site have a higher density and rank really well.
This site's strength is definitely its interior pages. The owner has a lot of unique content that is not shallow IMO. Daily updates occur and the site gets a good amount of traffic from repeat visitors (8,000 daily with over 50% being direct visitors).
Although my job here is to do the grunt work of fixing the meta tags, I'd really like to see this site perform better - with my help and the possibility of getting a long term client of course. Do you think the large number of duplicate homepage meta description tags are the reason why this site does not rank anywhere for its homepage?