With the increase of Customizable CMS like Worpdress, Drupal, Blogposts which can be used to make up a site in minutes, I think Google has given a flag to most common CMS Sites. While the HTML Sites (Like the 90s) are seen as Authoritative and has infact Rankings. Also Custom CMS if unique gives authority to the site under Penguin. I know HTML is a Turn-off for many Webmasters but with an old domain and Good Content, It is very Good in the eyes of Google.
I have been using this theory for 12 years, and it seemed to work up until Panda, and Penguin is worse! Still HTML.
CMS sites have in fact been negatively impacted with the recent updates but it is not about the platform itself. It's what people allow to be indexed. So many CMS platforms have so many dupe pages, archives, tags, categories etc.. It;s what is being indexed on the CMS sites that is the problem. Google is just saying clean em up. You're wasting their resources with a lot of dupe junk pages.
it's not the tool. it's how people use the tool. either it's PHP or pure HTML, these are just plain text in the sight of the search engine. it's how you structure the "text" inside.
I've never had a problem with my WP site getting ranked by Google. Those that are having issues with CMS sites are trying to trick Google. Just focus on putting good content and doing backlinks and this should allow the site to still get Google love.
Its not about the platform or CMS you use. It all matters with Optimization and the quality of back links.