Loki isn't Marvel's only great villain. Pierce was a fantastic villain and very underrated IMO, easily a close second to Loki. I think the direction they're currently going in with HYDRA has been phenomenal in TWS and AoS, and can really do wonders for future villains like Zemo, Strucker and (a new portrayal of) Red Skull. Also for all the crap people give Agents of SHIELD, they did have some really good and memorable villains. Lorelei was well done and the scene where she casually tells that guy to kill his wife was disturbing on first viewing. I thought Bill Paxton's character and performance were great, though he technically counts as HYDRA, which goes back to my point about having hopes for HYDRA villains in the future.
However, it's true that Marvel generally has had subpar villains. Bridges and Hurt gave great performances, but they didn't have much to work with. Abomination was fun seeing go toe-to-toe with Hulk, but was underused and needed a better design.
Vanko and Hammer were "meh". Vanko's reasons for doing all that make no sense past the first act and the film never explores the depth of his relationship with the Stark family. I kinda digged Rockwell's whole "he's trying so hard to be Tony Stark but failing way", but Hammer overall wasn't that impressive. You never felt he was more of a threat past being Vanko's *****, which would be better if Vanko, as the main villain, was better.
As much as I like Loki, I thought he was all over the place in Thor. It wasn't until The Avengers when he truly became great.
Red Skull and Mandarin were the biggest wastes of potential IMO. In the comics, Red Skull's fascism, ambition and imperial nature is horrifying. It's even been suggested he would have overthrown the entire Third Reich had it not been for Cap. Think of all the disgusting things Hitler did and believed, then imagine Red Skull on par or topping that. In the movie, he came off as a Saturday morning cartoon villain. He didn't feel threatening nor did he come off as a fascist. Yes, I know he was supposed to be one, but I never felt it nor did the film even explore that aspect of the character. Plus the way he got taken out was very anti-climactic. Kingsley's Mandarin was brilliant but...yeah, you all heard the story 1000 times. Been there, done that. Those two right there were huge losses on Marvel's part.
Malekith was boring and one-dimensional. Easily the worst villain so far. There was nothing memorable about him, and he is apparently a sadistic mastermind in the comics. Eccleston was completely wasted in the role.
I don't think Ronan is as bad as people make him out to be, I think he was good, but here's the problem...he's Ronan. As a deranged lunatic, he's fine. But why simplify someone like Ronan to a deranged lunatic? Changes from the source material are welcomed if the ideas are good/better. In this case, the change was not just pointless but detrimental. And much how like TWS/AoS brings great opportunities for future HYDRA villains, Guardians did the exact opposite with the Kree. The Kree are an imperial dictatorship and one of the strongest alien species in Marvel. In this, they felt like just another species. There was nothing that stood out past "blue humans", even in comparison to other aliens.
Ultron, Thanos, and Kingpin all look promising, so that's a good sign.