The problem is the motives and goals of the villains are not all that clear, nor is their methodology. Ronan the Accuser and Malekith suffer from screen time, so their threat establishment and empathy are diminished. Yellowjacket suffers from re-writes and motive changes – the lack of Edgar Wright and various re-writing is evident between the acts.

The MCU focuses on the heroes – particularly how fun they are – but that price gets paid in most of their cinematic efforts.

Even the villains I found weakest (e.g. Yellowjacket, Red Skull, Kaecilius) are good. The MCU movies are great and have lots of good baddies, but we’re not getting memorable bad guys in each and every movie that are as memorable as the Nolan Batman franchise villains.

The Vulture is probably the best film villain of the current MCU to date – which makes sense considering he’s essentially Tony Stark from Iron Man 1 pre-cave, but from the other end of things. Ego as a stand-in for imperialism is alright, but the weight is really carried by the converging narratives and character arcs (I quite like GotG 1 and 2). The Winter Soldier is more of an antagonist/plot-device than a villain. Hydra is more the villain in Captain America: The Winter Soldier, even though the climax is a fight sequence with the Winter Soldier. He’s not really the villain in that film. Ultron doesn’t get a lot to work with, and the menace is very ill-defined. There’s just a lack of clarity and willing to commit there that speaks to the heart of Joss Whedon’s works in general – something for a different time to discuss, really. I’ve mentioned Loki in a comment below 🙂

It’s possible I am missing what makes the villains in S.H.I.E.L.D. good, but I gave up on the show after a while because I did not find it or the characters enjoyable. I did forget Kingpin – which is definitely the best of DD by far, including Defenders which I didn’t really like for the villains at all.

Agent Carter, Agents of S.H.I.E.L.D., and all the Netflix series have had excellent villains (the masses of the Hand notwithstanding). Particularly Aida from the most recent season of S.H.I.E.L.D. and Cottonmouth from Luke Cage (along with Purple Man from JJ, but you mentioned you haven’t seen that one yet). Some of the villains were misses though, like Diamondback or Nobu. But even with the Hand, the villains in The Defenders were actually a great rogues’ gallery to set against the Netflix heroes (though the Hand itself still doesn’t make much sense).

Blade 1 is a good movie, though, so I don’t want to diminish this too much. It got too many mixed reviews for how good it is!

It’s really evident in the choice of Loki for the villain of the first Avengers. Here is a guy we saw beaten already, so something needs to be done to re-establish his threat. This is very poorly done, and is further exacerbated as a punch-line through the ending with Hulk.