Does not calculate SEO scores based on Live preview of the web page. So, in effect all the seo scores shown in the backend are incorrect as this is not what search engines would view and rate for the keyword.
Because of this limitation WordPress SEO plugin misses out on all custom page templates, carousel plugins, slider plugins, basically any plugin/shortcode which auto generates content in a page/post is totaly missed by WordPress SEO.
All the content which is stored in Post Meta information but shown in the post/pages front view is also missed.
Example 1: Your theme may add a title and a subtitle to a post. The sub-title is stored in a custom field in h2 tag. Missed in content evaluation.
Example 2: You create a Wonderful slider (Layerslider/Revolution slider etc..) on the homepage, with H2, h3 tags to attract information. Missed in content evaluation.
Example 3: You show contact information from the options panel in the header section of the theme. Missed in content evaluation.
Where WordPress is progressing as a CMS, this is a serious limitation of this plugin. Not all the information is stored in the WP Editor.