There actually isn't a difference between the two apart from their relation ship to the Joker. Both versions of her work equally well as a villain, an anti-hero, a straight up hero, a comic relief character, a psycho, a depiction of spousal abuse, whatever you want - both versions are that versatile. The only difference aside from their looks is their relationship to the Joker. Except even in the original cartoon there were stories of Harley trying to move away from him. So there's that.
Ultimately writers would be remiss to erase the fact that if the Joker ever REALLY wanted to, he could get Harley to fall in love with him again, just so so that he could use her and throw her away once more (this is why Suicide Squad: Assault on Arkham has the best, most complete portrayal of Harley's character to date); but having her character be that of an emancipated, self-reliant woman who is recovering from being the victim of abuse is a MUCH better, much more aspirational role for her, and makes for a far better role model for women in abusive relationships everywhere (honestly, what other character can claim to be inspirational to that group of people?), than whatever the fuck neckbeards like OP want her to be.
So I'm glad for Suicide Squad, glad for Birds of Prey, glad for the New 52, glad for nuHarley, glad for the new cartoon, glad for whatever she will be in in the future; because they will not only all be great, but they will continue in making OP seethe like a motherfucker :)