Mileena also has a 50% punisher, a no limit, fast, spammable projectile, a juggle containment move with a 4 frametick start up (compare with Kabal's 3 tick start up for the spin), bigger ground combos than Kitana, and a popup with potential relaunch ability on 4 characters above her, and look where she is.
Take Sonya (sweeper, big ground combo to juggle, +D+LKs) and Jax (sweeper, big ground combo, air throw) for instance, characters directly above her, they are sweepers with a lot of options in general as characters that compliment their built-in counter to Kitana. Sindel in general is an excellent counter to Kitana on top of that. These characters are above Kitana for a reason. If she were to advance beyond them simply because she might give Ermac or Human Smoke some trouble if they don't reliably time counter aaTPs vs her air fans, that would be a rather unreasonable move. On top of that, Robot Smoke air throw and invisibility, Kano sweeper + air throw. Kung Lao and Nightwolf's main disadvantage vs her is the no JPS to combo at all. Four out of the 11 characters above her have tough matches vs her but not distinct win scenario advantages, if she did, then she might have those advantages vs other characters as well. Some would even suggest that Kitana, Stryker and Scorpion are all a rotatable high-mid tier.
Edit:
A good comparison here is Smoke vs Scorpion, as in why Scorpion is slightly lower than Kitana and Smoke is way higher. The ground starting combo potential alone puts Smoke above most other other characters but mixed with his TP and air throwing tactics and bait, it enables him to be that top tier character. Scorpion's low combo potential is terrible, and so are just about all his potential counters vs Kitana. He still, however, has Smoke's tactics which keeps him at least mid tier. Scorpoion and Kitana might both have 50% punishers, but Scorpion's 50% is not readily available vs Kitana, whereas Kitana's is vs Scorpion. His TP counter damage vs her air fan is about 25%, relying only on TPing vs her will lead to stray fan lifts, or getting caught by fan throws that are behind him. That means you have to score this counter 4 times in one round, while avoiding the fans in general, with Kitana having little to no fear of ever taking any big damage, and that is a lot of effort. Whereas with Human Smoke, he has no dependence on his big punishers vs her, or anyone, and he only has to counter a fan essentially twice in a round (plus 4% more or so, but it is possible to get her into the corner virtually anywhere you connect the TP for over 50%)
