Plot hole: On 5/16/05, Ethan tells the judge that Gwen "has never shown any indication of a violent nature whatsoever." However, in October of 2000, Gwen locked Pilar in a closet and chased after Theresa with a baseball bat, and then attempted to viciously strangle Theresa. Ethan witnessed part of this attack. Even if he was willing to go into the courtroom and lie about that, why wouldn't Theresa expose the fact that he was lying?
Plot hole: On 1/10/05, Sam gauged Liz's coherence by asking her what year it was, and she responded 2005. But Liz collapsed at Sheridan and Luis' wedding, which was happening in part during Tabitha's New Year's Eve party. So how could Sam expect Liz to know what year it is? She wouldn't know if it's even past midnight on the day she collapsed, or if she's been unconscious for a day or more. And how did Liz get the answer right, besides?
Plot hole: On 10/4/04, Paloma met Chad and she explained that she knew all about what had happened with him and Whitney and the Cranes. But how did she know about that? She talked very little with her family before she left the Crane Mansion, and she wasn't present when Eve and Julian told Katherine about what had happened. Yet she talked to Chad about the situation as if she'd heard about it from someone close to the situation.
Plot hole: Flashbacks have now shown that when Martin Fitzgerald and Katherine Crane left Harmony, Paloma was a small baby, while Julian was a teenager. But if that's the case, then Paloma would have to be older than Ethan, who was conceived on Julian's wedding night with Ivy, which we're now being told didn't happen until after Katherine and Martin left. But Paloma is only eighteen as of August 2004, having just graduated high school. Ethan is at least in his mid to late twenties, having been a practicing lawyer in 1999.
Plot hole: The week of 5/3/04, Kay ruined the dress that Charity designed by changing the measurements before Charity actually made the dress. But the timeline made no sense at all. Charity and Miguel were talking about the dress and the fashion industry in the backyard until after it became dark, which in New England in May means that it was at least 8pm. Charity didn't start making the dress until after that. But how late could the Founder's Day Dance be starting that Charity has time to make an entire dress for it after 8pm?
Plot hole: When Luis got married at the end of 2004, Ethan was his best man. When Ethan was called away, his father Sam stood in. But why wasn't Hank Luis' best man? Hank has always been Luis' best friend, but when actor Ryan McPartlin took a role on another show, Hank just disappeared with no explanation.
Plot hole: On 5/3/04, Liz followed T.C. into his shed and saw that it contains the car that he was driving on the night of his accident. A year ago, Liz stole T.C.'s key and looked into the shed for herself, and was shocked by what she saw. But when she went in with T.C., she had to ask what that car was, because she barely knew anything about his accident, which is the truth. So why was Liz so shocked to see a car with a big dent in it? That's a very normal thing to see in a shed, I would think.
Plot hole: In the early months of the series, in the summer of 1999, Father Lonigan met many times with his longtime parishioner Grace Bennett, and a woman named Faith Standish who made several visits to town. Grace and Faith were identical twins who had been separated years earlier. Father Lonigan is blind, and usually recognizes his parishioners by their voices, yet he never noticed that Faith had Grace's exact voice.
Plot hole: During the 6/28/04 episode, Theresa is walking down a path towards a cliff when she comes across Fox. She then hides behind some trees so that she can eavesdrop on Fox without him discovering her. She decides to leave before Fox sees her and instead of going back the way she came, she runs straight towards the cliff (and where Fox is standing). Obviously, this is set up so that Theresa can fall off the cliff, but it makes no sense because she should have just gone back the way she came if she didn't want Fox to see her.
Plot hole: The Antonio-Sheridan-Luis triangle stopped making any sense a very long time ago. Antonio has been healthy since March, 2003, so there's no reason why anybody hasn't told him by October that Sheridan and Luis are in love (They couldn't tell him earlier due to his illness and the need to keep him very calm.). Furthermore, even though none of their friends or family said anything to Antonio, he surely would have heard by now. After all, the Cranes are front page news (witness the revelation of Ethan's paternity and the recovery of Sheridan from the ocean - the second time), so surely it would have been a huge tabloid scandal when Sheridan married the brother of her former fiancé.
Plot hole: On 10/2/03, LaToya walked up to Chad at the hospital and slapped him. But Puff Dog only gave her the address of the Crane apartment where Chad was staying, so how did LaToya find Chad at the hospital?
Plot hole: On 6/24/04, Martin and Katherine were in Mexico, reading a Harmony Herald article about Sheridan dropping the kidnapping charges against Luis. But that happened on the same day (not on the same day's show, but rather the same day in the characters' lives) as they were reading about it, so it would not have been printed in a newspaper yet. And even if it somehow had, it certainly could not have been transported to Mexico from a small town in New England on the same day.
Plot hole: On 3/16/05, Jessica demanded that her father Sam not call her mother Grace to tell Grace about what happened to Jessica. After that, Sam asks Ivy how Jessica knew he was going to call Grace, and this results in Ivy being exposed for having prompted Jessica's outburst. However, right before Jessica got upset, Sam told her that he was going to tell Grace what happened. That's how Jessica knew he was going to call her. Why would it be a mystery to Sam how Jessica knew he was going to do exactly what he had just said he was going to do?
Plot hole: Although Eve had told Grace about her secret past with Julian, she never told her that Liz was really her sister. She only told Julian, David, and Ivy. But in August, 2003, Eve and Grace began to have a conversation about the situation as if Grace already knew.
Plot hole: Theresa was convicted of murdering Julian Crane. But then Julian was discovered to have survived the shooting, and Theresa reversed her story and claimed that she only confessed to protect Ethan, whom she incorrectly believed to be the killer. Yet the investigation was never re-opened. I mean, I know Julian didn't actually die, but most police departments don't take very kindly to armed assault, either.
Answer: I don't know about good not wanting them to be together, but I know the evil side doesn't want them together because once they sleep together, then Charity's powers will multiply, and she will be a driving force against the evil darkside.