I voted for the ending Helicarrier battle, that's my favorite action sequence from the film. I like how they have essentially several battles going on with Cap/Falcon on the Helicarriers, Widow/Fury vs. Pierce, and Winter Soldier making his way into the fight and then final confrontations Fury/Pierce, Cap/WS, and Falcon/Rumlow. I remember I voted the ending battle from TFA as my favorite in final action scene poll in the Marvel Films forum. The setting and some of the action echos the flying wing stuff in TFA, Cap vs. The HYDRA aircrew in TFA and WS vs. The SHIELD groundcrew in TWS (Both scenes even feature a propeller/engine kill) and then the final confrontation vs. Steve/Buckey in the control center of the Helicarrier somewhat parallels the fight between Cap/Red Skull on the flying wing as far as the whole high altitude/top of the world setting. As far as which main event fight was better, Red Skull vs. Winter Soldier, it's no question the fight with WS. Even though we didn't get to see most of the Falcon/Rumlow fight I thought his comeuppance was brutal and satisfying. Over all it felt like a classic action/adventure climatic sequence, something you'd get from the older Bond films, even some of the Brosnan entries that I have a soft spot for.
As far as what was the best self-contained action scene in the movie, I would say The freeway chase, Cap/WS round 1. It's a really well done action sequence. The earlier chase with Fury is another one. Hell the action scenes are well done, The elevator escape and taking down the quinjet. If any action scene was a little underwhelming, it was the conclusion of the opening boat sequence. the fight with Batroc was well done, although it seems like Cap was pulling his punches. The ending was just kinda abrupt and it didn't leave as big an impression that I was expecting. Perhaps that's not such a bad thing. One of the few problems I would say I had with stuff like Skyfall, and other Bond/ or even the new Star Trek's it feels like they put all the big over the top climatic stuff at the beginning or first act so some of the later action kinda feels underwhelming. So I guess in a round about way the opening here is perhaps wisely underplayed a bit.
It's not really an action scene but I liked how the Bunker scene was kinda a throw back to the old school Bond Movie deathtrap troupe. I love pulpy stuff like that. Always happy to see the filmmakers include stuff like that. I wonder what kind of action we could expect from Cap 3? Maybe another propeller/engine/turbine kill at some point for good luck lol. I wouldn't have any complaints about another high altitude/aerial based climax again if they can come up with a good idea(spacecraft?), although maybe for the sake of variety they could have a ground based climax, might limit how much Falcon would be used. Or perhaps rather than an aircraft, a mountain top or tall building? Maybe an underground type base/lair/facility? I wouldn't mind seeing the Omega Base from Marvel Ultimate Alliance adapted, perhaps a shuttered underground SHIELD lab that can go rise up and go mobile on massive tank threads. If you've read the unproduced Indy 3/Monkey king script or are aware of it you'll know about the giant tank that was in that story. Would have been absurd from Indy(it became the tank scene from Last Crusade) but I could something like that working with Cap or Avengers, although Omega Base is even larger than the tank depicted in the Monkey King script. I know Kevin Feige was a producer on MUA so maybe we might see the Omega Base at some point as a nod to that.