If I were to put MCU's villains into tiers, it would go (in no particular order)
Good
Loki - exceptional charisma with just the right amount of petulance so it's entertaining watching him fail
Obadiah Stane - well acted, fits very well with Tony's backstory, albeit he feels very vanilla now after so many corrupt businessman villains
Red Skull - the best presence out of any MCU villain, he's got that swagger on lock. Weaving probably gives the best performance out of all MCU villains
Arnim Zola - fuck the haters, the brain in a computer thing in Winter Soldier was brilliant campy sci-fi. Toby Jones is pitch perfect as the meek scientist as well. His one on one with Tommy Lee Jones was fantastic in First Avenger
Winter Soldier - felt like an unstoppable force that bodied just about anyone who got in his way
Alexander Pierce - Redford was a great foil to Sam Jackson and really sold the hiding in plain sight philosophy for Hydra
OK/Competent
Ultron - Spader did a great job but ultimately the movie surrounding him isn't as good as his performance. He could have been great with a little tweaking
Darren Cross - as generic as they get but Stoll plays the deranged aspect of him so well, I still enjoy whenever he's on screen
Justin Hammer - just like Spader, Rockwell's performance is better than the movie he's in. I hope he comes back at some point
Aldrich Killian - whether you like the mandarin twist or not, Killian was well fleshed out with clear motivations and plenty of charisma by Pierce. It's too bad he went out like a chump . I'd really love for his head to be resurrected as MODOK
Nebula - she could be really good but didn't get enough screen time. Thankfully we'll see more of her in Vol. 2
Korath the pursuer - it's telling when a villains lieutenants are better than the villain. Hounsou is always entertaining on screen, which is more than I can say for Ronan
Crossbones - his role in Winter Soldier was just set up which will hopefully pay off. He was a solid mook
Forgettable
Whiplash - Rourke tried his best but aside from a few rare moments of genuine fun (JOU LOOSE, STARK), I don't care to see him ever return
Laufey - Marvel did him dirty, he died like a complete scrub
Terrible
Ronan - he didn't have the presence of Red Skull and therefore making him a religious fanatic felt flat and one note. His design was also garbage. What a complete waste.
Malekith/Kurse - who really cares about these two? Their motivations are vague and their elf language sounds idiotic. Kurse was a decent mook but overall, I didn't care for em at all.
Am I forgetting anyone? I feel like I am. Oh well. As a whole, the track record isn't stellar. I think the complaints are slightly overblown but the criticism is valid.
edit: oh yeah, Thanos. Personally, I don't think it's fair to judge him when he's had like 2 minutes of screen time tops.