That's easy... Sato Miwako. Super smart, sharp detective skills, and after what seemed like forever, she ended up finally reciprocating Takagi-san's feelings. Her side story has been quite humorous!
As for Haibara-chan, she is my favorite main character, and ranks second overall. To explain this, if you think about her life "before", she could only be seen as a villain. She certainly didn't seem to be objecting to testing APTX 4869 on a living "subject" (Numabuchi).
And yet, even in that evil, you feel sorry for her. Her parents dead (or so she believes... until DNA proves a corpse, you can't trust anything in this manga) yet her mother left tapes for her to listen to (still don't know the resolution to the secrets on those tapes... her Mom was what? and regret what?) and those tapes became the last connection to her parents. Her sister, also an agent in the evil organization, was murdered for trying to leave and save her little sister. Her life was totally controlled, and finally, she was sentenced to die in a poison chamber for speaking up against the injustice that the Organization was systematically killing off her family. (Well, she refused to do further research, anyway...)
She's been shot (what, 4-5 times now?), attacked, run over, beaten, but has bounced back each time to grow closer and gain stronger bonds with all of her new friends (even the Detective Boys, I think she sees them like little brothers/sister type characters in her life). Personally, I think she has a crush on Shinichi, even though she knows that he is totally infatuated with Ran.
Ai certainly seems to have one of the strongest personalities out of everyone in the series. She is also probably the only character that is more secretive than Shinichi/Conan when it comes to hiding her secrets. She is also, as I am sure, in possession of the keys that could unlock the shackles that hide the final secrets of the Black Organization. But her unwillingness to tell any of it to Shinichi/Conan in order to protect him is also exposing him to more danger, as he has to go to other means to uncover the secrets that she already knows. And I think that the reason that she so stringently hides those secrets is more to protect her parents’ memories than the more vocalized reason of “protecting” Conan.
So, to your point… yeah, she’s pretty cool.