OOOOkay. i'm not sure how best to explain it, but here we go.
The thing about Harley is, and I mean the true Harley not that monstrosity that was birthed with the new 52, is that she always had a dark side. The Joker didn't create her at all. He merely exposed what had already been there through emotional manipulation. In the wise words of Alfred, Harley was no angel. This is a woman that had no problem sexually manipulating her professors in college for good grades, even though her lack of proficiency could endangered someone. This is a woman who was planning on exploiting her patients with a tell all book for fame and fortune. In some incarnations she's even an armchair psychologist on tv a la Dr. Phil.
In spite of all this though, she's not the female Joker, unlike what some producers of the movie Suicide Squad have said. She's her own person. There's a reason why she didn't go with green hair and a purple suit when choosing her outfit at the Halloween store, and pre-new52 wasn't bleached but instead wore white makeup. True, she made herself over in his image but SHE made HERSELF. He didn't force her to do anything. She's his willing accomplice. She's not brainwashed either. Nor does she have Stockholm syndrome. People that say she does clearly don't know the meaning of the mental illness. If she's not in with The Joker she latches onto Poison Ivy and helps her with her schemes. Hell even Deadshot. Margot Robbie is right in describing Harley as a junkie, so I think she does understand the character on some level, but she's not just addicted with The Joker, it's with the life of crime in general. She views their (H,J,PI) lives as glamorous fun.
Which leads into my next point. Harley does not want to be "normal". AT. ALL. That scene with Jared Leto and Margot Robbie holding babies and kissing was a bunch of bull crap. Yes Harley wants a family with The Joker but she wants it on her terms.
. Not with some random Joe Schmoe. In fact in "My Boyfriends Back" The Joker starts treating her right, telling her how much he loves her, etc etc and you know how she reacts?? She doesn't want him anymore!! In fact she goes to great lengths to get him back to the way he was before.
I think Suicide Squad was on the right track with Harley's character by having Harleen jump into the vat of chemicals instead of be thrown by The Joker and scream "nooo" but it's contradicted by him torturing her first. Which is just another thing that doesn't make sense from scene to scene.
Anyway, i'm not very good at doing write-ups on characters so I hope this makes sense.