Keep in mind that this was roughly 10 years ago, and whether Mileena was more iconic than Sonya 10 years ago does very little to tell us whether she is more iconic than Sonya today. These things change.
I genuinely wonder what the current ranking is, although, of course, it is impossible to measure. The only thing that seems certain is that Scorpion, Sub-Zero, and Raiden should still be the top 3, probably in that order. Nothing's happened to shake them out of the public consciousness - they continue to be a big deal in MKL, they continue to get plastered all over the marketing (Scorpion on both covers), starring roles in the games (Raiden as final/10th chapters), or both (Subz has 2 chapters in MK9 and is all over MKX trailers).
After that, it gets real murky real fast, IMO. Any one of Johnny, Sonya, Liu Kang, Kitana, and Mileena has dibs on #4, although, within that, it's tough to see Sonya above Johnny or Mileena above Kitana. Then - and I'm just guessing here, of course - the third tier is something like Goro, Kung Lao, Jax, Shang Tsung, Shao Kahn.