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I feel we are missing some information here. For example, for our site we have done a canonical on the pages where we have query parameters. We have also specified these parameters as representative URL in Google Webmaster - URL parameters. Even after this we received this message "Googlebot found an extremely high number of URLs on your site". The surprising thing is that these parameters are existing on the site for a long time, and the total URL count is reducing. Even after this Google has started sending this message to us since Feb 2014. Seems there has been some algorithmic change because of which some additional conditions that have not been highlighted in this thread have to be taken care of.. Not sure what..