I thought Killian was a great villain with a good motivation and plan. The twist was genuinely shocking and well plotted.
I am a big fan of Guy Pearce and I do like his casual nature in the film. The twist works because Kingsley sell the hell out of it. But the motivation, plan and execution are Acme level. Tried, test and eventually blows up in your face.
But yes, HYDRA and their use of Winter Soldier was also great. That's the thing, TWS is different in that it doesn't really have a singular "big bad". Basically, the whole "establishment" is the big bad.
That is what I call good writing. If you are going to solo your villainy you better bring a Darth Vader, Joker, Loki, Bane, Silva, etc.
Still, IM3 was a great character piece. Stark's arc was brilliantly done. In TWS Steve doesn't really have an arc. Not necessarily a negative, but because he's a static character, interesting as he is, it allows for more characters around him to shine. IM3 was simply about Stark and his journey, and it was one of the best in any comic book movie in my eyes.
Steve has an arc in TWS. It is as strong as Tony's in IM3, while actually engaging other characters. Steve's entire identity is questioned. For the first time since waking up he has been forced to learn how to "live" and to do so in a time that does not agree with him. Captain Steve Rogers has the ultimate version of PTSD. He is seemingly only comfortable on a mission, when given an order and asked to act. That seems to be because no matter the time and era, orders are still the same for a soldier. And then as the curtain begins to part, he starts to realize that even those orders aren't what they use to be.
There is also the question of what others are asking from him. Who is Fury asking him to be? Pierce? Natasha? One of the reasons I think Sam has been getting so much love, is that he takes the role of the audience. He does not question Steve. He fully embraces our Captain, and follows him into the breach without a second thought. He is a borderline Captain America cheerleader, but then you have those heady discussion about what it means to stop being a soldier, and if it is even really possible.
Arguably the best thing about TWS is that it was able to tell a story and allow everyone involved to play. And it pays massive dividends. Natasha's arc is pretty great stuff, and the same with Fury.
So for me, IM3 and TWS are Marvels best films. For different reasons.
TWS
TFA
Avengers
IM
Thor
IM3
TIH
TDW
IM2