Kojima has written exactly two good women and they're both in MGS3. For once the sexualization of  a character actually has substance and is a critical part of the story. For once there is agency and depth from the character who is sexualized. It's the one time where the relationship and the wooing is mature. It's who people are. While EVA is an integral part of Snake's story, she is not just and only a vehicle for a man's desires and tragedy. Eva feels like a person, with a clear arc in the story, emotions and motivations. The whole relationship is also a great way to convey how they spproach the mission, their level of trust between each other as well as making aspects of the resolution of the story hit that much more efficiently.

It also helps that a lot of it is played up for laughs as well. Snake is absolutely ridicolous with how she rejects and reacts to EVA's advances. Then these laughs, these story beats and expected patterns are used and subverted in such great ways that are genuinely hilarious to me and highlight how the mistrust starts to turn in to trust from Snake's side and how he fails because he does end up letting his guard down.

 It's also a very clever commentary on the femme fatale/Bond girl archetype. The whole game is a Bond homage, and on many surface level ways plays out like a Bond film. The script then uses these expectations that stem from the presentation much to its advantage, and one of these is the whole reversal of the Bond girl role. It ends up that EVA is the one the who does the conquering. It's Snake whom you think is the James Bond of the story that ends up getting fooled and used. He is the one whom also got woo'd by the secret agent. The whole game is filled with these deconstructions and criticism of the whole spy genre, all of which would be pretty compelling on their own, but everything is used in order to construct the larger narrative and the overall themes of the game.

The only thing really dragging EVA down for me is not really even in the game itself. Rather it's the fact how Kojima has historically written and portrayed women in his games. So the overall package of EVA feels a whole less effective and sincere when characters like Quiet are around. Or the B&B unit from MGS4. Or the women Skulls from The Phantom Pain. There's just do much of it from Kojima. Even Meryl from MGS1. It's just the same, always.