Waters is terrible on speed option, there is no doubt there (though he did improve as the season went along).
However, he's pretty good on zone read option and delay QB lead/draw plays. He is good at moving in the pocket to buy time to throw as well. He's not a detriment as a runner and the QB run game can still be a nice part of our offense, it just won't be the percentage it was for Klein or Sams.
The comparison with Matt Miller is almost spot on. Waters is actually a slightly better runner than Miller, Miller had a higher completion percentage, but Waters has a higher YPA. Their TD:INT is identical.