Mileena's x-ray does 33% on it's own. So to me, doing a combo into it that does anything less than 40+% is a waste of meter. (She does have one that does 48% I believe.)
Mileena's X-ray can be very important to her in certain matchups. (ie: Noob, Reptile, Kitana). But NOT in a combo. Sure she has near 50% with the right X-ray combo, but the problem is, Mileena's combos have a lot of hits and give the opponent a lot of meter to use breakers. The best thing about it is, her X-ray is her only armor move to break through frame traps and zoning.
Mil's meterless combo damage is such that, generally, if your opponent guesses wrong 3 times they die. And because her X-ray does like 3% less than most of her BnBs, you've effectively reduced the amount of wrong guesses to two instead of three. If you have full bar and you've taken more than half your opponents life, Her X-ray becomes very scary for them since it's basically a one-hit BnB. (It's also the longest range move she has that isn't roll).
Thinking about it, what would be cool is if you could combo a roll after it ends. She does pop them up in the air with her knee, so it wouldn't be unrealistic to tack on a roll, b1,4, neckbite or roll, b1,4, telekick, sai for about 40 something percent.