But IMO, every single one of the MCU villains had a LOT more going on than "I'm a bad guy who does bad things for bad reasons," including the ones you singled out as not very good.
Stane (Iron Man) wanted to continue building his own private empire, and turned on Tony when Tony made it clear that Stark Enterprises could not longer be manipulated as his front. Not bad. Very "real."
Blonsky/Abomination (Hulk) was a bit power hungry and was driven insane by the serum. Again, not bad. Typical villain stuff. Probably my least favorite villain, but he was still fun to watch. And, really, the main conflict in the movie was not so much any "villain" as Banner trying to deal with himself and the government not understanding and hunting him. It wasn't really a villain-driven movie.
Vanko and Hammer (Iron Man 2): Motivated by revenge and jealousy toward Stark. I found both of these motives to be well-developed and credible. Solid villains.
Loki (Thor): Excellent villain. His motives are a bit complex, and to this day, we aren't
entirely sure of what he wants because he is playing it somewhat close to the vest. But it stems from him wanting to rule Asgard, whether because he is jealous of Thor as the heir-apparent, or because he is half Frost Giant, or because his childhood was a lie, or because whatever. The Frost Giants also bear mentioning as well. Their motives simply boil down to age-old feuding with Asgard, and being put down and (in their view) oppressed. Even though it isn't explored that deeply, it doesn't need to be because (1) we can identify with that, and (2) they are really the second-tier villains behind Loki anyway, so we don't care.
Red Skull (Cap): Just a fanatic. He wanted power, for himself and for Hydra. Given the context of the movie where he was essentially a Nazi who was more extreme than the Nazis, and the context later established for Hydra in the MCU in general, this worked even though in all actuality, he was not very deep. Solid villain.
The Avengers: Back to Loki. Awesome. He plays it like he wants to rule earth. But he plays it so well that we don't even really care whether there is some deeper motive. And, of course, there is. Anyone paying close attention to the big picture knows that what he REALLY wants is to rule Asgard. And his motives make sense. And he is so cool that, again, we don't care.
Killian (Iron Man 3): Pretty cool. He wanted power because he was a creative mind that could come up with a way to grant himself that power, and Tony spurning him ended up twisting that in a very sinister way. He absolutely worked as the villain for me. And I for one loved the Mandarin plot twist. Who we thought was the Mandarin was sinister and fearsome. The fact that that specific individual ended up being a bumbling, toothless fool does not diminish that, for me. It makes the one who orchestrated it all appear sinister and fearsome, albeit in a different way. I think this was very well done. And the fact that the real Mandarin is apparently out there kind of makes me a bit giddy.
Malekith (Thor 2): Similar to the Frost Giants. But add in the fact that the Dark Elves really were all about unleashing the aether since day 1. I mean, we don't know why, but it sort of takes on an air of them sort of being an aether death cult of sorts. Kind of hard to relate to, but not completely. That was their thing. I dunno. He isn't all that deep, but I have no problem with Malekith either. I didn't really need him to be any more than he was for the movie to work for me.
Pierce, Winter Soldier, Crossbones: Hydra. Politics. Power. Works for me.
Ronin (GotG): I thought he was pretty cool. Yeah, he could have been fleshed out a bit more and made better. It kinda feels like he would have been the easiest to give a bit more development to, which makes it kind of feel like Marvel dropped the ball on him a bit. But he was still pretty fearsome, and his motives weren't really that difficult to understand: He is a fanatic and a rebel/freedom fighter/terrorist leader/whatever. Not to mention, he is prideful, and resents being Thanos' minion, so it is easy to understand why he embraces wholeheartedly the power of the orb when he has an opportunity to seize it. He absolutely worked for me. Where I
do feel like Marvel actually sold a villain short in this film was Thanos. But I know Marvel is playing it a bit close to the vest with him, and there will (hopefully) be a lot more fleshing out of his character later, so I can forgive that.
Ultron (Avengers 2): He was cool. I felt he should have been more, but he was cool.
Cross/Yellowjacket (Ant Man): Pretty much Stane 2. And I'm fine with that.
Zemo (Civil War): His character development took a back seat to the main conflict in the film, which is a bit odd, since he orchestrated the entire thing. And that's fine. It worked. He actually had a pretty complex background and set of motives, and even though we were only given a glimpse of it all, there was more than enough there to make it all work.
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I dunno, I could nitpick any of these to death. But in lining them up, it's a pretty impressive slate overall if you ask me. Some are definitely more developed or more relatable than others. But the ones that feel like sort of B-grade villains are still not bad. And the ones that I feel added a lot are a pretty sizable majority. And, yes, I am a bit of a fanboy as well. But that doesn't mean I'm wrong.
EDIT: And I can't believe I actually took the time to do that.