It is more disturbing to see the same amount of reports even on clean or new system. Findings of Advanced Mac Tuneup states that system performance keeps on diminishing due to presence of adware, junk files, duplicate objects, and useless items occupying huge amount of hard disk space. Is CleanMyMac legit or is it a scam or virus? I haven't had any system issues with Clean my mac but then again thats just my experience / opinion. Also you can manage disk space with Storage Management in MacOS El Capitan, which available at About This Mac Storage Manage. This tool also helped me a lot to move rare used.
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