edit: Just to be clear, I'm not making any positive or negative statements about the article, I just wanted to help you work out what it was you had missed, and I think what I described is it.
We just had the biggest recession since the Great Depression. Taking such a short window will of course show wage deflation. You cannot remove the effects from bubble income and expect to keep bubble income.
The overall trend for most slightly bigger windows is wage increase. If a certain wage level meant middle class in the 1960s, or 1970s, or 1980s, or 1990s, then we have a larger ratio of people in that class, not less.
Of course if you define middle class as also increasing in income, then you can play all sorts of tricks. But the fact remain more people than perhaps any but the last decade are richer than ever. All your graphs point to exactly this.
Remember - bubble popped. It takes a while for those effects to smooth out.
http://www.advisorperspectives.com/dshort/charts/census/hous...
Also, I think you would be better linking here, which has several versions with differnt groupings (per @r00fus' point) as well as the full discussion behind it:
http://www.aei.org/publication/census-data-on-income-distrib...
It's interesing data, but also missing the last 5 years which are crucial as this is a recent phenomenon. The 3rd chart in the series I think best shows what economists are calling the "lost decade" where we stopped making real progress in upward mobility. Add another 5 years onto those series and I think you would see we are going backwards now.
Edit: Shouldn't the top graph in my link be the same as your link? Now I'm doubting these graphs are even 'correct' (methodology aside)