Ok, lets give this a go, this will be along post, I'm a data analyst so i find this stuff interest. The main point is, because 1 statistic is not enough to show something as complicated, with as many variables, as how good a champion is. For example, I could use your argument to say Robert Horry is a better basketball player than Michael Jordan, he's won more championships, so does that mean he's better? No, because you are ignoring a lot of variables such as skill of teammates/coach, number of years played, quality of competition, etc. etc. 1 variable cannot be used to determine something with so many variables. I'm not saying win rates is useless, but it is not enough on its own.
So the most common argument is that popular high pick rate champions have lower win rates than they should, where as low pick rate champions have higher win rates. So lets look at a couple possible supporting arguments.
Let's say the breakdown of players playing Lee Sin and Karthus look like this:
Lee Sin: First time players: 30% 2-5 times: 40% 5-20 times: 20% 20+ times: 10%
Karthus: First time: 5% 2-5 times: 20% 5-20 times: 25% 20+ times: 50%
With everything else equal, who would you expect to win more? Obviously Karthus because the players are more experienced.
So again, THESE AREN"T REAL NUMBERS I have absolutely NO IDEA if this is the case, but it is a plausible reason for why they would have a lower win rate. You know who does have this data and can do a proper analysis? RIOT, which is why I trust them over random forum people.
Lets take another example, lets say Champion A is always picked first and get counter picked in every game, where as Champion B is ONLY picked as a counter pick, which champion (everything else being equal) do you think would have the better win rate? Obviously champion B because he is put in a better position to win each game.
Again, this may not be the case, but it is another plausible explanation.
Anyways, those are juts 2 quick ones that come to mind, the arguments themselves aren't the point, the point is, win rates is not enough information to decide which champion is better because it ignores sooooo many other variables. No data analyst will take 1 number like that and draw a conclusion, you take that number, it is opposite of what you expect, so you dig deeper to try and find out WHY it is opposite.
We don't have enough data for these things, RIOT does.