I don't think this will be a case like Lost, Heroes or Battlestar Galactica, where after the excitement dies down, people realise the shows were messes. Breaking Bad will be ranked alongside The Wire, The Sopranos, Deadwood and Six Feet Under as one of the best modern TV shows.
I also don't think the show ever tried to be realistic. It was frequently absurd, over the top, and comic book. It's part of the charm.
I would definitely not include Deadwood and Six Feet Under on a 'Best shows ever' list. Six Feet Under had a great first season and great last episode, and otherwise was a cyclical predictable mess of directionless sex and death. And I think most of the anger at Lost and BSG were from the entitled 'Any ending that isn't the one I wanted retroactively ruins the entire show' Comic-Book-Guy-criticize-alike crowd.
But yeah, even the entitled whiners were happy with Breaking Bad, I think its legacy is safe.