I would say this matchup is 6-4 in Mileena's favor. There are a lot of really annoying things about it. Sometimes it's difficult to low fireball her sais. You'll trade if you don't time it right. If the opponent is expecting the low fireball though they could do some stupid teleport stuff. Her d4 is frustrating to say the least. Even if you do risk jumping back and throwing a quick fireball you might eat a full combo if they're expecting it.
I play this matchup very cautiously. Most of the damage I do is off straight up punishes or off an instant air fireball when she's trying to do a bunch of d4s. That strat won't work against everyone obviously. My recommendation is to know your best punishes for each situation. Naked tele kick. Tele kick with a delayed sai. Roll. Etc. Try to stay within the 4,4 range and whiff punish if possible. If you manage to get her in a combo, try to keep her standing so you don't have to deal with wakeups unless you're baiting them out. End with a 311 instant air fireball. I find keeping her grounded and up close isn't so bad. Otherwise she has too much control.
I don't fight too many Mileenas but that's what I generally try to do. It might not work against someone really good. There's only 1 or 2 people I can think of in my area that even use her. Online the matchup is the worst since I can't punish a blatant teleport for the life of me if there's input delay.
If you don't know a punish or need help. Just think simple. Off a blocked roll you can do a 1~scream combo and then work your magic from there. Off a tele, the timing will differ but you can do a variety of things. You could do b12, 1, b2 followup, d1 ex scream. You have options. It just depends on what the precise situation is. I would practice them all (easier said than done). D1 into ex scream I find is a very very important thing to learn in general. I can land d1 anti-airs but I usually fail to follow up with anything when in a pressuring situation. That's something I need to work on. If I ever get a chance to sit down and actually play -_-