Bringing someone back from the dead goes against the very nature of things and thus they can never return as normal.
Mary has some brain damage from lack of oxygen before the Emergency Transformation. Her personality is thus radically different and she ends up "off".
Mary was brought back in the same body she died in, without anything being done to fix said body after her death. Since a dead body not only cannot heal, but begins to decompose (and this is assuming that there hasn't been any kind of funeral preparation; if her dead body was embalmed things would only get worse), this means Mary is forced back into a body that's in no kind of shape to support life, which is agonizing at best.
Mary was a deeply disturbed individual before her death, but becomes more 'normal' and healthy after being brought back.
Mary returns, good as new... But contact with the unearthly forces he had to harness in order to perform the resurrection caused John to Go Mad from the Revelation or become a victim of Demonic Possession... and having been effectively Unpersoned due to her death, Mary has nowhere to turn for help.
John and Mary's friends were afraid something would go horribly wrong with his attempts to bring her back, but she seems to have come through it just fine.
Alternatively, Mary's body doesn't quite come back right, but her mind and soul remain unaffected, and she's still the same person she was before after taking a bit to adjust to her new circumstances.
Double Subverted: ...But her 'good' condition soon deteriorates, getting worse and worse.
Parodied: Post-resurrection, Mary has become a cackling, Obviously EvilVamp running around wrecking havoc... and John doesn't see anything wrong with her or her new 'hobbies', explaining everything away with increasingly inane excuses.
Zig Zagged: After the worry and the deterioration, we find out that was just Mary messing with them. Which was out of character...and a symptom of her coming back wrong.
No one is brought back from the dead.
Everyone is revived with no major change in demeanor.
Enforced: "We need to show why they can't just revive everyone."
Lampshaded: "Told you Mary wasn't going to be the same,"
Invoked: When Mary was killed, the murderer laid a curse upon her to screw with any resurrection attempts.
While Alice was alive, Carol hated her, and even now that Alice is dead, Carol can't let it go. So she forces Alice back to life, and she uses the most traumatic method she can find to do it.
Exploited: Mephistopheles uses this for a two for one special. Bob sold his soul to resurrect Alice. He knows she'll come back deeply scarred and will likely make a deal herself to get revenge on Bob.
Defied: John refuses to bring her back — or, rather, to use any method of bringing her back with even the slightest chance of having some negative effect on her.
Discussed: "That won't work. You can't just undo death like that without consequences."
Conversed: "Oh, now I get why they don't just resurrect everyone who dies..."
Deconstructed: Mary comes back from the dead "wrong," but becomes attached to living as this "wrong" self she has become because it is infinitely preferable to being dead. She resists any attempts to change her back or end her life "to set things right again." This causes a schism amongst her friends and family between those who wish for her to remain "wrong" because she has chosen to be that way and those who wish for her to die again because her state causes them great sorrow.
Reconstructed: Her "wrongness" further corrodes due to the nature of being a resurrected person to the point where she becomes too "wrong" for her to have an opinion about her own state of being. All agree that she has been irredeemably corrupted by her resurrection.
Plotted A Good Waste:
Mary was brought back wrong because, deep down, John doesn't want her back. The fact that he has to face this starts up the next arc.
John misperformed the ceremony, and now has to go on an epic quest to set it right.
Played For Laughs: Mary used to be a natural blonde — now she's a brunette. Much to her horror.
Played For Drama: A demon piggybacked on Mary's resurrection to get into the mortal realm, and is hijacking her body while working to weaken the veil between worlds and usher in a new age of terror, while holding what remains of her soul as a bit of blackmail against poor John.
You could try to bring back Came Back Wrong, but it's probably a better idea to just let it go.