I don't think that win rate is the only way to go with this. look at the win rate for the all ranked - the highest is rumble, but he's played in such a small percentage of games. that means that the people who play him are probably only those who are really good with him, so it gets skewed. if you look at number of games played, ez is by far the most, but he is 12th as far as win percentage goes. Compared to twitch (same role) who has a higher win rate by a full % point, but ez has like 16x more games than twitch played, which is more impressive in my opinion.
browsing around on that looking to see if i can see something that matches my personal experience, i think that looking at the overall win numbers under the popularity bars looks about right. Once you get past teemo, jax and darius, the overall number of wins settles down pretty quickly. Darius isn't even that high compared to jax and teemo. Its well known that jax is a strong champion in dominion, even if he isn't the biggest problem, and teemo is a major issue and that shows in his total won games being 70k higher than jax's and 130 k higher than the average of most of the other champs in the top 15.
interestingly though, if you look at it that way, it actually takes the all ranked values much longer to settle down into a consistent number of won games - i'd say jax and sona still have significant advantages in terms of wins over the rest of the visible champs there and they are in 6th and 7th place. So as far as OP champs, i'd say there might be more of an imbalance in ranked than in dominion, as we have about 3 and ranked has about 7, just according to how i'm looking at the data there.