Minako is odd. Right from the moment she asked if he loved shopping, he knew he was dealing with an odd Lilim. Her relentless cheer isn't something he's used to, coming as he does from the EVA universe, and he's still kind of peeved about how she talked to him after the 'attack' on Asuka - like he was a child, or simple or something, just because he doesn't understand Lilim emotions and social rules.
All that said, he doesn't dislike her. She's just not the type he's likely to feel any sort of kinship toward, because they're so wildly different, and his lack of feelings will contrast sharply with her nature. He'll still be as pleasant as he is with anyone else if she persists in seeking him out.