SPOILER ALERT: This will contain spoilers for all of Agents of SHIELD,
but especially for the midseason finale of season 3.
Agents of S.H.I.E.L.D ended the first half of it’s third season by killing off one of its main characters – and easily its main villain – on a deserted alien planet and, supposedly, leaving the corpse of Grant Ward there to rot after Agent Coulson crushed his chest.
Of course, that the show would take such a turn really was not obvious from its’ first episodes, when Coulson and Ward where on the same team, everyone believed HYDRA to be a thing of the past, Daisy was “just” a hacker slowly turning into an agent, Fitz 
and Simmons were still Fitzsimmons and a budding romance between Ward and Daisy, whose name at that point was still Skye, was one of the driving aspects of the show – so driving, in fact, that there are watchers and fans of Agents of S.H.I.E.L.D out there who, no matter what Ward did and no matter how clear Daisy made it that she did not want to be with him, still insisted that Skyeward (their shipname) was meant to be.
And it is kind of understandable: The dynamic between Daisy and Ward was set up beautifully in season one, with Daisy as a young, optimistic, kind – hearted hacker slowly turning into a S.H.I.E.L.D agent with the help of her grumpy, seemingly-cold-but-secretly-caring Supervising Officer Ward who did not open up to anyone but her. It’s a classic dynamic, really, the sullen man with a tragic past geting healed by his lady love, and we see it in quite a few popular ships, like Sandor Clegane and Sansa Stark, Draco Malfoy and Hermione Granger/Harry Potter, River Song and the Doctor, Tony Stark and Pepper Potts, Jaime Lannister and Brienne of Tarth or Mai and Zuko, just to name a few.
But Agents of S.H.I.E.L.D quickly turned that dynamic on its head by what was probably the most dramatic reveal of the first season when Ward shot Agent Victoria Hand, freed John Garrett and turned against his team in support of HYDRA.
This development radically changed the relationship between Daisy and Ward, making them players on opposing teams (though only on of them knew that at that point in time), but more importantly, it also changed the lens through which their previous interactions were seen by the audience. Re-watching the first season with Ward’s true position as a member of HYDRA in mind makes it far easier to spot him manipulating the team, but especially Daisy, something he even admits when asked about it by Raina in 1×18, Providence: “Skye was the unknown variable. Being her S.O. put me in a position to be a sounding board, get an idea what she was thinking.”
One of the scenes in which this manipulation, in retrospect, becomes quite obvious is a scene in the episode before, when Daisy and Ward hide in a utility closet while trying to free Simmons and Trip and take back the Hub from who they suppose are HYDRA agents. Daisy is supposed to go to processing center to hack it, but there are several armed agents in the corridor which Ward plans to take out. When Daisy alerts him to the fact that this will likely be suicide, Ward says: “Not if I don’t die. And if I do… maybe I deserve to. I killed an innocent man, Skye.”
Who Ward is referring to here is Thomas Nash, a man that Ward killed in episode 16 and that he claimed to believe to be the Clairvoyant, the evil mastermind that the team had been up against so far. According to him, Thomas Nash threatening to hurt and kill Daisy – who had already been shot on his orders before – got Ward so angry that he killed an unarmed, wheelchair bound and defenseless man.
However, as we later learn, the Clairvoyant is John Garret, a level 8 S.H.I.E.L.D agent who used to be Ward’s SO and under whose orders Ward was working, meaning that he likely knew Nash to be innocent and killed him to tie up loose ends and make the investigation into the identity of the Clairvoyant seem finished. And even before we learn of Ward’s true allegiance, Ward makes it clear that he does not, in fact, regret killing Nash (as he did it for the protection of his team). Regret and remorse are emotions he only portrays later on and only around Daisy, who reacted with horrified disbelief to Ward killing someone. Telling her that he thinks that he deserves to die shortly before going into what seems like a suicide operation to enable her to fulfill her part of the plan is emotional manipulation – Ward is preying on Daisy’s compassionate, understanding and forgiving nature by not only telling her how he feels he should die for killing an innocent man (something he knows she found horrifying), but by then also telling her that he only did it because he thought she was going to be hurt.
This is what he does: Ward manipulates people to his advantage again and again and not just Daisy: He sleeps with May (who he deceives about who he actually is, withholding information from her and making informed consent to sex on May’s part impossible) during his time as a team member to cloud her judgment because he sees her as the primary threat
and, when Jemma jumps out of the Bus to protect the team, he saves her as a selfless act of bravery to gain their trust. After he is revealed as a member of HYDRA, he returns to his team with the express purpose of either manipulating Daisy and the rest of the team into helping him crack her hard drive so that the Centipede Project’s phase 3 can use the data on it to advance or killing the team and taking Daisy prisoner. And by telling Daisy about the abuse his parents and older brother inflicted on him and telling her that he is not a good person who believes he may not deserves happiness, he is again preying on her compassion and support to get her to trust him. In season 2, he tries the exact same thing again to elicit compassion from Daisy, who is interrogating him about HYDRA while he is a captive of S.H.I.E.L.D and later on, after breaking out, threatens to kill Daisy’s friends to get her to come with him to meet her father against her explicit will. He also manipulates and abuses Kara Palamas, an ex – Agent of S.H.I.E.L.D who was captured and brainwashed by HYDRA, by promising to help her rediscover herself and enact revenge on the people responsible for her captivity and torture, but ultimately using her, making her torture others and then killing her accidentally. And in season 3, Ward recruits the son of an ex – high ranking HYDRA member with the promise of money and power, but is after the secret family vault all along and quickly discards him.
Of course, manipulating people into doing what he wants is not the only crime Ward commits – that list is far, far longer and includes, apart from murdering uncounted nameless and named S.H.I.E.L.D agents: dropping a containment unit containing Fitz and Simmons out of a plane and into the sea which lead to Fitz sustaining permanent brain damage; threatening to rape Daisy; trying to kill Melinda May multiple times; kidnapping Daisy twice and touching her multiple times against her consent; using a mother and her child as well as a whole bus of civilians as a human shield by strapping a bomb to himself and threating to detonate it if S.H.I.E.L.D tried to take him in; torturing his older brother and killing him as well as his elderly, immobile parents in a house fire; torturing Bobbi Morse with Kara’s help as a punishment for Bobbi handing over the coordinates of a safe house she thought was unoccupied to HYDRA while working there undercover; setting up a death trap for Lance Hunter that almost killed Bobbi; brainwashing a member of HYDRA to follow his commands; threatening to kill Andrew Garner, May’s ex – husband, to stop May and Hunter from coming after him; torturing another member of HYDRA after said member failed to kill Andrew Garner; torturing the employees of a HYDRA member for information while talking about how much he loves that; blowing a hole into a passenger plane to jump out of it with a parachute which likely lead to that plane crashing and innocent, uninvolved civilians dying; torturing Simmons and threatening to kill her to get Fitz to do what he wanted and taking Fitz onto an alien planet with the express purpose of using him as bait for a murderous alien.
Ward’s actions, apart from showing time and time again, that he cares most about himself and his own gain, also show that he does not care about how his actions harm others. Of course, Ward often has justifications for what he does – S.H.I.E.L.D and the team have become his enemy and he needs to enact revenge against them/he must protect himself by killing and/or endangering others – but even then, these justifications betray an inevitable disregard for human lives.
This is a stark contrast to the compassionate Daisy who was a member of the Rising Tide and then became a S.H.I.E.L.D agent to protect people. When she gained super powers in season 2 that she could not control and that could end up hurting people, she shot herself with an ICER and then used gloves to suppress her powers which ended up hurting her. Daisy cares about people a lot, even about people she does not know, she values their lives and safety and she is willing to put her own life on the line to protect others.
Ward and Daisy are almost polar opposites – which is to be expected, after all, considering that Daisy is one of, if not the, 
protagonists of the show and Ward is the main antagonist. The fact that they have such differing values is what allows the conflict between them to exist, but it is also something that makes it almost impossible for them to ever become a couple, in addition to Ward continuously manipulating, kidnapping and threatening her and her friends.
Don’t get me wrong: People being on different sides in a conflict does not mean that you can never ever ship or that they can never ever become a couple. It just means that one of these characters has to change drastically to make it possible, either the “good” character has to become evil or the “evil” character has to be redeemed, and that in a believable and plausible way.
But in the case of Ward, redemption has long been an impossibility because Ward never actually regretted any of the things he did and always found justifications or people to blame, and even then it is doubtful if Daisy would actually forgive him, considering that she explicitly said that she never would. So the only other option is that Daisy becomes evil and joins Ward’s side, meaning HYDRA, and that is even less likely or plausible than a Ward redemption arc because it would go against everything she stood for from season 1. Really, the only plausible option for Daisy to become evil and involved with Ward at this point would be her getting kidnapped and brainwashed and that would do a massive disservice to her character and arc.
Of course, apart from the fact that they are on opposing sides of a conflict, there’s the fact that Ward manipulated and abused Daisy. He left crucial aspects of who he was out to get her to like him, he lied to her and threatened other people to get her to do what he wanted, he touched her against her will, he kidnapped her twice and he threatened that, because she woke up a weakness inside of him and made him want her, he might “take what [he] wants, wake up something inside of [her]” – which is a rape threat packaged nicely in some victim blaming.
And ultimately, that is more important than the fact that their value systems differ so much: Wanting Daisy to be with Ward is like wanting Sansa Stark to end up with Joffrey Baratheon or Petyr Baelish. It means wanting an abuse victim to end up with her abuser.
