Phase 1:
1) Loki
2) Iron Monger
3) Red Skull
4) Abomination
5) Whiplash
Brief explanation.
In Avengers Loki was a fairly generic (but charismatic) villain however in Thor Loki was excellent. He had a relationship with the MC, displayed feelings and affection for multiple characters (including Thor) and you understood why he went bat **** crazy.
Iron Monger was a fairly generic villain in motives but the dude (no pun intended) is just so damn likeable, riding a segway with a cigar, offering pizza to Tony (but limiting it to two slices, cause he was angry).
Red Skull was also fairly generic in motivation, but he was similarly played very well by Weaving (very charismatic), had a dope design to boot.
I think the concept behind Abomination was cool, an old veteran who feels outdated and wants to stay at the top (at the cost of anything). He did come off on the more generic side, but the template was there.
Whiplash also had a good template and started off very strong (great motivation and reasoning, better then Tony at being Tony), but after he gets captured the first time I forget pretty much everything he does lol. I understand they had troubles with the actor which I assume is why he was neglected to the sidelines, it really is a damn shame.
Phase 2:
1) Ultron
2) Aldrich Killian
3) Ronan
4) Yellowjacket
5) Alexander Pierce
6) Malekith
Ultron is the only genuinely good villain in this phase. The concept behind him was cool, he had some very sharp dialogue and Spader made him very charismatic. He also had a decent amount of depth, like showing care for Scarlet when she was in danger and sorrow when the twins left his side. I think what really detracts from him as a villain is his lack of presence (I didnt feel him as a threat) and his end game, which was frankly just dumb.
Killian was decent, I liked the concept behind him, wanting to control things from the sidelines rather then being at the forefront. I also felt bad for him and its understandable why he did some of the stuff he did. That said he never truly had a great scene, his dialogue was never anything special and his fighting abilities weren't that enjoyable. He also the replacement for the actual Mandarin smh.
Ronan is pretty bad, had a few funny moments towards the end but thats because of his reactions to the Guardians more then himself being funny. He did feel like a threat at least but jesus was he generic.
Yellowjacket was also just straight up generic, I honestly dont remember much about him which says a lot.
Alexander Pierce who? I mean seriously I vaguely remember him cause he was in an awesome movie but man was he forgettable in every way.
Malekith? Garbage. Doesnt get much worse as far as villains go, Kurse was better and he didnt even talk.
Phase 3:
1) Thanos
2) Killmonger
3) Vulture
4) Zemo
5) EGO
6) Hela
7) Kaecillius
Thanos was the best villain in the MCU, he was the first time we saw a villain as essentially the protagonist of the story. You understand why he is doing what he is doing even if you dont agree with him, he shows plenty of depth (with his relationship with Gamora) and he respected his opponents if they deserved respect (like Starlord and Stark). He was also a threat and felt like it and literally won in the end. It really doesnt get much better.
Killmonger was fantastic, you understood where he was coming from and he forced the MC to change his ways (i.e. fuelled the MCs development, which is the objective of a villain character). He was also charismatic and a truly GOAT death scene.
Vulture was the everyday man, he was relatable. He was a bad dude but he has his morals, not evil for the sake of being evil.
Zemo was amazing on paper, but in the grand scheme of things the thing that prevented him from being higher is his remarkable lack of presence in the story. His motivations make sense and the fact that he can break apart the Avengers where other super beings have tried and failed is note worthy.
Ego was dope, dude just seemed like a cool dude (basically Starlord 2.0)....until he was revealed to be an egotistical planet destroying planet. Very akin to Iron Monger in many ways as a villain and what made him work.
Hela was cool, generic af but she made it work with her charisma and presence. Definitely felt unstoppable .
Kaecillius is the only real *bad* phase 2 level villain in this phase. He had a few funny moments but man was he forgettable, he was basically a Dormammu henchmen and it showed. If he came back then he has room to grow, as it stands hes not good.
Overall it goes Phase 3 >>> Phase 1 >> Phase 2 villains.
1) Thanos
2) Killmonger
3) Loki (Thor movie)
4) Ultron
5) Vulture
6) Zemo
7) Iron Monger
8) EGO
9) Hela
10) Red Skull
11) Aldrich Killian
12) Abomination
13) Whiplash
14) Ronan
15) Kaecillius
16) Yellowjacket
17) Alexander Pierce
18) Malekith