There is less proof for Ai not liking Mitsuhiko than for Conan not liking Ai. When Ai sprained her ankle in the woods in the ep. Mushrooms, Bears, and the Detective Boys, Mitsuhiko helped her walk and bandaged her ankle. She complimented him sincerely, even calling him her "outstanding rescuer". It might have been to make him feel better, but Ai has never complimented a little kid like that before. On the other hand, Conan is too busy thinking about Ran to like Haibara more than a very good friend. I guess it depends on whether or not Haibara decides to take APTX4869. If she doesn't, then 10-20 years later, Mitsuhiko will be more mature and they would be almost compatible.