The two girls are vastly different. This is apparent from the outset. Abigail displays an uncompromising and even disrespectful attitude towards adults at the beginning of the play, as illustrated in her response to her uncle's questions when she says:
No one was naked! You mistake yourself, Uncle!
Abigail deems herself the equal of adults as shown in her attitude to John Proctor. When he wants to convince her that their liaison is a thing of the past she responds in anger:
I know how you clutched my back behind your house and sweated like a stallion whenever I come near! I saw your face when she put me out and you loved me then and you do now!
Abigail has been corrupted by her adulterous relationship with John Proctor. She also feels empowered when her accusations of witchcraft against whomever she chooses are believed. When her motives are questioned, she is clearly not afraid to express her opinion and does not shy away from confrontation. She is even daring enough to threaten Judge Danforth when she tells him in Act 2:
Let you beware, Mister Danforth—think you to be so mighty that the power of Hell may not turn your wits?!— beware of it!
Furthermore, Abigail is cunning and revengeful. She wants to punish those she feels have done her wrong. She implicates Elizabeth Proctor, for instance, by acting as if she is a victim of an insidious and supernatural attack by her. Abigail wishes to get back at Elizabeth for firstly, dismissing her from service and secondly, from denying her access to John, whom she still desires. She is intent on having Elizabeth be executed because she believes that with Elizabeth out of the way, she would have free rein when trying to reignite her affair with him.
Abigail is malicious. She accuses many of witchcraft because she enjoys the power it gives her. This malice is also evident when she threatens the other girls if they should tell the truth about their actions in the forest:
Let either of you breathe a word, or the edge of a word, about the other things, and I will come to you in the black of some terrible night and I will bring a pointy reckoning that will shudder you.
Abigail is plainly not afraid of manipulating the truth or others. She is intent on covering up her transgressions and will do everything in her power to avoid discovery.
Mary Warren is afraid and naive. She does not have any of the turpitude displayed by Abigail. She comes across as honest and wants the girls to tell the truth from the beginning:
Mary Warren: What’ll we do? The village is out! I just come from the farm; the whole country’s talkin’ witchcraft! They’ll be callin’ us witches, Abby!
Mary Warren: Abby, we’ve got to tell. Witchery’s a hangin’ error, a hangin’ like they done in Boston two year ago! We must tell the truth, Abby! You’ll only be whipped for dancin’, and the other things!
She also later truly believes that she is doing good when she testifies against those whom she thinks are witches. She is easily controlled by the court's injunctions and, in line with her respectful nature, does as she is told. Her childish nature is evident in her little argument with John Proctor about going to bed.
Proctor, in horror, muttering in disgust at her: Go to bed.
Mary Warren, with a stamp of her foot: I’ll not be ordered to bed no more, Mr. Proctor! I am eighteen and a woman, how-ever single!
Proctor: Do you wish to sit up? Then sit up.
Mary Warren: I wish to go to bed!
Proctor, in anger: Good night, then!
Because Abigail is such a strong and dominant figure, the mild-mannered, kind, and respectful Mary does not stand a chance against her. Mary only agrees to testify against Abigail at John Proctor's insistence. Her innocence, however, is evident when she, unlike Abigail, is unable to put on an act when asked to.
When Reverend Parris asks her to faint in court to prove that their accusations were all part of a charade she cannot and states that she does not have a sense of it. Abigail, on the other hand, can easily act as if she is seeing spirits. She makes it seem so real that everyone believes her.
It is Abigail's vindictive nature and her perfidy which, ironically, wins in the end. Marry succumbs to the force of Abigail's will and her convincing act to such an extent that she ends up accusing John Proctor of witchcraft.
Abigail Williams is a leader and Mary Warren is a follower. The court attempts to treat all of the girls as equal victims of witchcraft. The court does an okay job with treating all of the girls the same, the court greatly favors Abigail as a key witness. It's why she is called into the final court sequence with John. No other girls are called in. Just Abigail.
Further evidence of Abigail being a leader and Mary being a follower is given in Act 2, when John tells Mary to tell the truth to discredit Abigail.
Mary Warren: She'll kill me for sayin' that!
In addition to that scene, Mary still fears adults and authority. Because of that, Mary consistently tells the truth. The worst that she will do is not say anything at all, but Abigail will blatantly lie to get her way. She's a dominating presence and Mary is simply a useful sidekick at best.