My sparring partner mains Mileena so I know your pain all too well. I don't use Reptile but I think the best overall approach is to try and bait the hell out of that purple bitch!
Only throw your projectile when you guys are a FULL screen apart, she can only do two things at that point, Teleport Drop or the roll. If she teleport drops on reaction there's really nothing you can do, but at least it won't lead to a huge punish. If she tries to roll while a full screen away, she won't reach you, she'll stop right in front of you and start to recover, that's where you can unleash your most devastating combo.
When I throw projectiles, I'll throw like 2, do a quick punch just to make them think another projectile is coming out, then quickly block, usually the opponent thinks I'll throw a third and try to roll or teleport drop, but when I block them I can punish. So mix it up by throwing 1 2 or 3 projectiles, a fake out punch, and immediately blocking. NEVER projectile spam Mileena.
Another nice way to bait, is just to rush up on her after a knock down, but block when you get right next to her. You'll be able to punish any wake up attack at that point.
Another thing that helped me was learn to BRUTALLY punish a blocked roll. I used to get nervous that I would mess up a combo on a blocked roll so I'd just uppercut instead. That won't cut it against Mileena. You gotta punish that roll hard as hell. In training mode, put her wake up attack on and sweep her till you get that roll, and practice till you can punish her roll as much as possible without even thinking about it. If possible see if you can time your combo to start just as she lands so you can do a full "from the ground" combo which are usually more powerful than "from the air" ones.
Also, when up close and blocking, just block UP the whole time, NEVER down. The worse that could happen is that she hits you with some weak low attack which you can just recovery roll away from. Other than that you are completely safe from her Up + 4 combo starter, and completely safe from her roll which can be blocked high.
I don't think there's anyway to really punish a blocked teleport drop other than a quick jump kick sometimes.
Important as well is to not let Mileena chip your life away with her constant sais so remember to just duck and not block when she starts spamming her sais.
BE PATIENT! If Mileena'a only game plan seems to be throwing out a barrage of sais, just duck and wait calmly. Don't always try to dash block to get close. If you wait long enough the opponent will probably get restless and try to get close where you'll have more control.
Hope some of this helps!
