I haven't seen all of these, but I get the impression that the conversation here mostly focuses on either Akatsuki or the Royal Guards, and between them, I think that the Guards and Meruem are much scarier. Akatsuki is comprised of exceptional Shinobi, but they still play within the frame of what's considered possible in the ninja world. They are terrorists, kill indiscriminately and are pretty fucking evil. But that's something the ninja world is sort of used to. In terms of power and maliciousness, they are bad news...but sort of calculable.
The Royal Guards and Meruem on the other hand are genuinely treated as an alien, unknowable entity, a new top dog on the food chain. This is true for their warped minds, but also because of their off the charts power. In a setting that had thus far been so careful about strategic application of powers and the importance of tactics, these guys felt like they were breaking the scale. When Pitou first appeared, everything about was what the kids call "aura". Everybody was scared shirtless, she killed you know who with apparent ease and then we learn there's two more like her and her king.
From an in-universe perspective, the Royal Guards are much scarier.