How much of Mileena's advantages actually overpower him enough to the point where it doesn't feel even at all?
Zoning? Mileena doesn't realistically stop Reptile from advancing at all. It's not dashblocking he uses to get in...Reptile can duck any standard projectile and dash immediately past it...and the entire sequence is very fast. Please throw a standard projectile at me...I will duckdash it so fast and be right there in your face. And he can pace her in projectiles, as well as check her anti-projectile options (Yes, he's using meter, but again, Reptile gains meter VERY easily). It's very even here.
Footsies? D4 is very identical on both parts, but unless you're standing, she has zero followups that leads to free extra chip damage. Reptile has a number of them. She can check d4 with her u4, and you can check her d4 with b4. However, you can also check her d3 as well with it unlike her, and 321 can be used to bypass a greedy Mileena hellbent on d3ing you. Also, Reptile has faster advancing normals than she does, and f2 leads to combos as well. And Reptile can very easily whiff punish Mileena d4. Mileena also has no answer to point-blank forceball (She literally has no powerful punish for it), so f2 xx forceball = godlike vs her. Her only advantage here is the faster d1 and d3, and the fact that u4 leads to damage. Reptile, though, is faster elsewhere, and in general powers his meter by playing footsies. Everywhere else really is even. They both have checks for each other.
Pressure? Mileena's weak point is straight up her lack of armor. d1 isn't cutting it anymore defensively...it's getting counterpoked reliably now. She can roll underneath some things, but not everything. d4 only gets you so far defensively, too. Reptile, on the other hand has dash, and EX slide defensively, as well as d4. Her faster d1 and d3 helps here, but she's gonna have situations where she wishes she had armor. It's even here, simply because Mileena can pressure Reptile and force him to be riskier, but Reptile can put her into scenarios where her lack of armor bites her in the ass.
If Mileena does have an advantage, it's only a 5.5-4.5 advantage, which is basically even, just slight edges. But personally, I don't see it anymore. When you really understand where Mileena falls apart and see what Reptile's options are overall, he doesn't really have it that horribly. Yes, telekick jail sucks, but the way you'll be playing the matchup, it really shouldn't even be that much of a factor because she won't be using it. She'll be too busy playing footsies to even care about it, really. Me and Death going back and forth says a lot. There is no advantage on either side. Just need to start grinding out the matchup.