I was thinking more along the lines of there being a difference between a person that is a villain, as in they are bad, and more the old concept of "the villain", as in the primary antagonist of the story. Not all films a have a "villain" in this sense obviously, but superhero films have traditionally relied very much on a main antagonist to provide the plot and action, perhaps supported by a secondary antagonist (or more). Loki's role in the plot is usually a bit more complicated than being a traditional main antagonist. That Dark Elf was in the role of "the villain" in Thor 2 for example, not Loki, who was more a treacherous ally of the protagonist, even if he is still a villainous person. He is probably the main villain in Thor although the King Of The Frost Giants fits that too. In The Avengers Loki completely fulfills the role of the traditional primary antagonist imo (and even there he is framed more as a pawn of the leader of the Chitauri, but he has so little presence I'd count Loki as the primary antagonist), though incidentally I think that's Loki's worst film and could have used a different primary antagonist.
Of course maybe there's something to be said for Marvel relying less heavily on each superhero film basically being its villain ("The One Where Batman Faces The Joker", "The One Where Spiderman Faces Doctor Octopus"), but the fact remains that in my opinion if you go through the list of MCU main villains you don't get that many great or memorable ones, and their best one (Loki) is actually at his best when not playing the role of the Big Bad. It hasn't been much of a hindrance to them so far because many of the films have been introducing us to new main characters for the first time, and The Avengers had a bunch of different heroes interacting for the first time, so those films haven't been as dependent on a villain for their plot. I don't think it's a coincidence that two of the worst received films in the series were simple direct sequels (Iron Man 2, Thor 2), the type of films that could really have used a more interesting or memorable villain. Captain America 2, although a sequel, benefitted from a different setting for its main character and did a better job with its antagonists (The Winter Soldier was a pretty cool memorable "physical antagonist", and the old guy in the suit that is in charge of the organisation you work for being the villain may not be too original but it works well for action movies). And I think a big part of what made Iron Man 3 better than 2 was the... interesting approach taken with the antagonist(s).
By doing lots of different film franchises to keep things fresh, Marvel might be avoiding the need to rely on strong villains to stay good (you can bet they'd need a villain with the impact of Heath Ledger's Joker to stay successful if instead of having just had a 10th MCU film, we had just had Iron Man 7), but as we get into more direct sequels I'd like to see some better villains ahead. Though as has been pointed out to me, the best / most known Marvel villain IPs seem come from X Men and Spiderman so the MCU might not have great source material to work with...