With seven seasons on the air, first season.
While other villains have come and gone, including aliens in possible futures and Hydra leaders from the past, these two remain fan favorites. There are a lot of reasons to appreciate them both as the best Agents Of SHIELD villain.
Ward: His Betrayal Of SHIELD
Small seeds were planted throughout the early episodes of the show that allow fans to trace Ward's villainy. He had the "highest marks since Romanoff" when it came to espionage, he had a tendency to shoot first and ask questions later, and he had a troubled childhood. That didn't entirely prepare fans for him to reveal himself as a mole for Hydra.
His betrayal of SHIELD created a major turning point in the show. SHIELD was destroyed from the inside out, Coulson's team had to go on the run, and dynamic of the show made a serious shift.
Raina: Introducing The Inhumans
Raina's search for "blue angels" and her quest to introduce Skye to Calvin Zabo is what ushers in the era of the Inhumans on the show. Without Raina's meddling and manipulation, Skye would never have ended up with her ability to quake.
When Skye and Raina underwent terrigenesis, that also introduced the audience to Afterlife, an Inhuman settlement that would come into play again in the final season, and to the backstory for Daisy Johnson. Skye transforming into Daisy has been one of the most compelling parts of the show's narrative.
Ward: His Betrayal Of The Team
With Raina, it's made clear from the beginning that she's on the bad guy's team. With Ward, that's not clear. He formed attachments on the team. May was in a relationship with him, Skye had a crush on him, and Fitz and Simmons looked up to him.
When he was revealed as Hydra then, it made the turn personal for the audience instead of just another villain in the show's arsenal.
Raina: Her Attempt At Flirting With Coulson
When Raina found herself in a sticky situation in the second season, she did what she did best - tried to her best to manipulate her way out of it. She did it in her signature style, but she tried her technique on Coulson.
Agents, who were listening to Coulson's meeting with Raina wondered aloud if she "flirting with him," to which Agent May responded, "that's her thing." Despite the seriousness of Raina's situation, it provided for a bit of levity for her character since Coulson already knew exactly how she operated.
Ward: He Took Over Hydra
With both the Avengers on the big screen and what was left of SHIELD on the small screen going after Hydra, there were really only a few splinter groups left in the second and third seasons of the show. Ward decided to step out of the shadow of the man who mentored him and strike out on his own, forming his own version of Hydra.
Ward's methods might not have been great - essentially creating a fight club for those who wanted to - but it was a change to see him striking out on his own instead of continuing the motivations of those he learned under.
Raina: Her Intellect
Raina wasn't just someone following orders or on a quest for power. She asked questions to better understand what the plans of others were. She also did the work herself to achieve her own ends.
It's Raina who saw the ins and outs of the experiments with Project CENTIPEDE. Raina understood the science behind it, understood the implications of the invention of Gravitonium, and worked to understand her place in the world of the Inhumans. She was always interested in learning more, fascinated by the way science and "magic" intersect.
Ward: His Match Against Coulson
When Ward truly embraced his villainy, he targeted Coulson specifically. Every chance he had to get under Coulson's skin, he took.
Again, Ward's storyline as a villain became more personal to the audience as a result. Coulson, as the character that drew most of the audience to the show from the movies of the Marvel Cinematic Universe, was the everyman they wanted to root for. When he was miserable, the audience felt it and wanted revenge as much as he did. Coulson going to another planet and taking the opportunity to end Ward's streak of villainy was exactly what the audience wanted.
Raina: Her Flower Dresses
Raina had the benefit of being a civilian character so she didn't spend most of her episodes in tactical gear. Instead, her clothing reflected who she was as she donned her flowered dresses as a kind of camouflage.
Each of her dresses was unique for her appearances in the series, but she always made sure she disarmed her targets by asking if they liked them. After all, "everybody likes flowers." Raina approached her wardrobe as an extension of her con.
Ward: His Backstory Was Extensive
Though Raina's backstory - her grandmother's stories of blue angels, her surviving on the street - was hinted at throughout the show, it was never detailed. Ward, on the other hand, became a fully three-dimensional character thanks to his fleshed out backstory.
The audience didn't just hear stories of Ward's childhood from his brothers, but actually got to see his teen years via flashback. We saw the moment John Garrett took him under his wing and the moment Ward committed to Garrett's cause.
Raina: She Just Wanted To Know Her Path
Part of the reason Raina was such a compelling character was that every choice she made wasn't about being a leader or grabbing power or gaining revenge. Raina wasn't out to be a villain. She just wanted to know her path - what she would become.
Raina had been fed stories of blue angels in her childhood and of glorious transformations. She just wanted her shot at fulfilling her destiny, whatever it was. Raina wasn't even upset when she realized her destiny might have been protecting Daisy from her own mother in the end.