The Marvel Cinematic Universe is the king of franchises, having made over 10 billion dollars in 8 years. Not only have they made some of the most popular films in the last decade and have created a trend in superhero movies and shared universes.
An issue fans of the comic books have with these Marvel films and TV shows are the villains (90% of them) with the most common comment being "it was good/great if only they could make a good villain it would of been amazing!!!"
I have made a list (well more a rant) to explain why the problem is there and how to fix it.
Focus is an important problem that Marvel suffers from. The "Marvel Formula", as it has now been named is the technique and style that Marvel have developed over the years to the point it has became second nature.
When the MCU started it didn't have any heavy hitters, all their characters were considered B to D list characters. So Marvel had to make great character driven stories to make you like the character you knew nothing about, they added some humour and action set pieces and doing so they dropped focus on the bad guy. That made it so the attention is on the hero as that is the guy who will be returning in future movies and felt they didn't need to expand the villains role, and they was right for some time.
Look at a film like Ant-Man that features a seriously unknown hero, extremely cheesy concept and hard to make cool, but they were able to pull it off and that is because they took time on the protagonist, making the science semi believable and for that film they didn't need to focus on Yellow Jacket, people went another wasted/pointless Marvel villain and absolutely forgetting the fact it was a 2 hour film about a guy who talks to ants and was extremely successful granted the villain wasn't that good but really didn't need to be for the story.
And that is really the problem Marvel's been having, their characters aren't known to the main stream audience at all (until they have a movie that is) and spend time compensating and making it all about the Hero.
Now people might think that because I said that they over compensate the focus on the hero because they are less known characters, that their sequels would focus on the villains as they are made the hero "main stream" making better villains as they can focus on the villain more, but marvel hasn't done that either, actually done the opposite in the case of Thor who had the strongest villain in Phase 1 with Loki and the weakest in Phase 2 with Malekith (below) from Thor: The Dark World ( in my opinion the weakest of any MCU villain).
How do you fix the focus?
1) There are many ways the MCU can fix their focus, the main thing they shouldn't do is kill the villains. at the beginning of the MCU villains were killed off without a second thought and granted they weren't the best villains but keeping them allows them to develop as characters, Look at Zemo from the latest Captain America: Civil War he was barely seen in that movie and wasn't focused on but was introduced in a way it sets him up for future Marvel movies (Hopefully setting up Masters of Evil/Thunderbolts).
2) Marvels strongest movie villain is arguably Loki from Thor/Avengers and a good reason for that is his interaction with the main characters, as Thors adopted brother he was able to be focused upon more as the brother rather than the villain. A technique Marvel should use again in further movies like Captain Marvel or Ant-Man and the Wasp as even though they are great characters even I a hugggge Marvel fan couldn't tell you what villains they would/should have but if they was focused in a similar way to Loki it would make them stronger characters.
3) Now I will admit making a villain a key character in a movie as well as the supporting characters in a 2/2&half hour movie is hard but their is a format which the Marvel villains have been rocking and that is on the small screen.
Marvel & Netflix has been rocking the Bad guys with The Kingpins & Kilgraves and shockingly this season of Agents of S.H.I.E.L.D gave us Hive (a surprisingly good villain who intentionally/unintentionally is exactly the same as Apocalypse from X-men: Apocalypse accept he looks much cooler and and is developed greatly) these villains are unknown when compared to the likes of Lex Luthor, The Joker and Loki but they became some of the most fear/hated villains that Marvel has made because they have time to develop them, the Netflix shows have around 13 hours of entertainment which is enough time to develop these villains.
This Would Suggest that they have kind of solved the problem in their own way but unfortunately they haven't because in Daredevil Season 2 who's bad guy was? The Punisher? Electra? The Black Smith? Nabu? To this day I'm not sure and I loved season 2 of Daredevil but there was this flavour missing that season 1 had with the Kingpin and in season 2 it jumps between the story lines to try and fill the gap that he left but at the climax of the season it was disappointing as their wasn't a pleasure of when the hero wins against the villain.
Originality of Ideas and Motivation (OIM)
OIM for a villain is important, extremely important and is something marvel have struggled to explain with there villains for some time (for the movies that is),
Lack of Originality
If it isn't the genius understudy/rival/partner that steals the protagonists idea to mass produce the idea as a terrible weapon (Iron Man - Iron Monger, Iron Man 2 Justin Hammer & Ant-Man - Yellow Jacket). It's the ruler of a army that isn't happy with how the world has turned out and wants to change it in their image (Captain America: The first Avenger - Red Skull, Avengers -Loki, Thor the dark world - Malekith, Captain America: The winter solider- Hydra, Guardians of the galaxy - Ronan and Avengers: age of Ultron - Ultron).
The only villains not to fit into this stereotype of unoriginality and have decent motivation is The Incredible Hulk's Abomination which is all about POWER, Iron man 2's Whiplash who wanted revenge on Tony for his father screwing over Whiplash's father, Thor's Loki who's plan was to get the affection of his adopted father, Iron Man 3's Killian who had a virus (never explained good enough in my opinion) and Captain America: Civil Wars Zemo which was a scheme to break the avengers and is the only successful one.
How to fix OIM?
Well it's hard to say how do you fix motivation and originality of villains but the best thing to do is look at the list of best cinematic villains and their motivations, with the fans best comic book villain being Heath ledgers Joker who's motivation was what? Well, that's the weird thing about it - there isn't much to say about the jokers motivation apart from because he can. what The Dark Knight showed is that you don't need an over complicated plot device for motivation and/or plan for the villain. Unlike Ultron with it's (yes it's an it) humans who ruin this world the only way to protect them is to kill them motivation. so I will drop a city out of the sky plan, don't get me wrong it was cool to look at but a overly complicated Idea.
The Plan/Idea concept
Having a villain, with a simple goal sounds too obvious and boring but it seems to be make the best villains. my favourite villain, Hans Gruber from Die Hard (below) who's plan was so simple people looked past it and thought when he took people hostage and was called a "terrorist" it would be a ransom type situation when in fact his plan was pretty simple, have hostages to stop police interference and rob the place. Nowadays Villains have to have these complicated plans people think you have to go BIGGER to be better when it isn't needed.
Heck Marvel isn't the only one with a villain problem, DC have the Joker (who is being rebooted/redone),
but This is just my opinion