There was a difference between John Cena and Stone Cold and that's their gimmicks and the way there were portrayed. Stone Cold was an anti-hero and a straight brawler, a pub fighter. He just went their and beat the living hell out of the other guy and it worked. Austin could also cut fantastic promos, was a great worker and appealed to the teenage demographic. And stone cold could however still put on a fantastic contest, Austin Vs Bret Hart was a fantastic Match.
John Cena is different. He almost always wins clean, and is to be honest a kind of a super hero. Yes Stone Cold's wrestling skills weren't the greatest, neither was the Rocks but they had soo much more about them. Stuff that John Cena doesn't have. Cena doesn't have the second to none Mic skills that the Rock had, and he didn't have the gimmick that Austin had. That's why his flaws are more visible. Stone Cold however was a fantastic pro wrestler.