What you're actually arguing is that some stats (the ones you don't like) aren't accurate enough for your satisfaction. That's fine and all, and it's something of a point (essentially that, in sports, compiler a/k/a cumulative stats are often a lot less meaningful than other types of stats) but that's not new ground, and it's an essentially hollow argument. Nobody looks to total yardage in a game and says "I can't believe Miami won that game, when they were out gained 300-299!", and nobody looks at total yardage in a season as the signature stat for which team will win the Super Bowl.
But, if you want to get a decent start at figuring out which offenses/defenses were best, or worst, total yardage isn't a bad place to go. It's not perfect, you can usually find exceptions, and context is important, but it can be a good indicator.
2017 NFL Team Total Stats - National Football League - ESPN
2017 NFL Team Total Stats - National Football League - ESPN