The fridge page for the first film notes that the paint on Cap's shield represents America; easy to superficially damage, but covering an indestructible plate beneath, and easily repaired with some attention. See the poster for Winter Soldier: Paint, gone. Shield, unbreakable. So, the plot can be inferred; Cap is going to receive a No-Holds-Barred Beatdown, but. HE. WILL. NOT. FALL. Also, the metalic gray color of the shield can be inferred as Graying Morality of the situation.
Note the changing of Cap's color palate throughout the movie. When he's working for SHIELD and not quite sure what his purpose is, his uniform and shield have a darker color scheme. But as the movie progresses and he starts fighting for the virtues he believes in, he first starts using the classic red, white, and blue shield before finally donning his stars and stripes inspired World War II uniform.
The Winter Soldier seems to be wearing greasepaint around his eyes and a mask that covers his nose and mouth, but not his hair or forehead. This is an exact inverse of Cap's helmet, which only leaves exposed the area around his eyes and the lower half of his face (Note that the Winter Soldier's design was lifted almost completely from the comics).
Black Widow mentions working for the KGB, but it's said that she was born in 1984. The KGB disbanded in 1991. In The Avengers after the little girl has successfully lured Dr Banner to the house on the edge of town, he sarcastically references the child's tender age. Natasha replies that she started at a similar young age.
In The Avengers, it was very convenient for Loki and the mind-controlled SHIELD agents to find such a large amount of freelance scientists and mercs willing to battle SHIELD for them, wasn't it? But considering that SHIELD was infiltrated by HYDRA, these highly-trained operatives could have very well been HYDRA agents that joined Loki willingly and brought all their knowledge of SHIELD and its super-science along with them, teaming up with him only to betray him when he was no longer useful.
Loki's rhetoric about The Evils of Free Will and the old German man telling him "There are always men like you" becomes even more poignant when Zola explains this to essentially be HYDRA's philosophy.
That Spoiler Title? The identity of the Winter Soldier? The twist that every fan can see coming? All just a distraction from the REAL twist - that SHIELD has been infiltrated by HYDRA.
In the center of SHIELD's office, an eagle statue is very prominently displayed in a very Roman-esque fashion. This has always been a symbol of America so it's not too unsettling but this one is ostentatious to the point of being ominous. Then you realize with HYDRA being a part of SHIELD, the Nazi-esque usage of the eagle makes perfect sense. You might also notice Director Fury's standard MCU outfit bears a striking resemblance to that of one Johan "Red Skull" Schmidt. Makes you wonder if he wore it at Secretary Pierce's suggestion...
In the tie-in comic to Captain America: The First Avenger, it has a scene where the Red Skull reveals the MCU version isn't a white supremacist. No, he's just a mass-murderer. Pierce's friendship with Nick Fury may be genuinely sincere as they're fanatics obsessed with order but don't necessarily hold any racial supremacist beliefs. It also widens their recruiting pool considerably. The Red Skull's brief rant about a "world without flags" at the end of The First Avenger also gains greater meaning in hindsight, as an indication HYDRA isn't about swastikas or blue eyes blonde hair, but simply about power and order.
Zola's recruitment of allies to join HYDRA seems like something which wouldn't work. Obviously, people would be watching him. However, he's a computer. If Zola talks about the kind of people they need to recruit and the threats they need to take down, who is going to believe he's a threat? The movie also illustrates the kind of people who believe in the Evils Of Free Will are the kind of paranoid types who are attracted to SHIELD in the first place. The Security Council played right into HYDRA's hands.
If Zola was able to create an algorithm that can accurately predict who would be a likely threat to HYDRA, it's only logical that it would be also able to do the opposite and predict which people would be receptive to joining HYDRA. HYDRA was able to expand its base of agents without risk of exposure because they knew in advance that they were only asking the people who would say "yes."
The part where Steve speaks French — he could've picked that up from Jacques Dernier, the French member of the Howling Commandos. It might also be in part to his embarrassment over misunderstanding "fondue" in the first film.
All of a sudden, Obadiah Stane's business deals with terrorists seem a lot less like war profiteering and a lot more like being a member of HYDRA, which has the expressed goal of creating threats in order to prove the dangers of Free Will. It could have even been him who set up the accident which killed Howard Stark.
So, why did Fury decide to take Steve down to see the almost finished Project Insight? Because he was having his doubts and was trying to give Cap a heads up in case things went bad. Maybe acting as a Secret Test of Character too, seeing if Cap would hold tight to his ideals.
Fury comments that Pierce turned down a Noble Peace Prize, saying "Peace isn't a prize, it's a responsibility." At first it seems like a moment to illustrate how good Pierce was at hiding his evil, but then you realize that he actually believed that. His goal was always peace, but at the cost of complete control of the world.
Now we can guess why Fury valued Coulson so much, even though he was seemingly just a really good high tier agent and people like Sitwell could have easily replaced him in the organization. If someone gives their life for the cause and actively resists being saved from death, then you know they aren't a spy and have no ulterior motives. Compare Sitwell, who was mentioned by Garrett to have never been seriously injured in the line of duty.
Remember what Fury called Coulson when mourning his loss in The Avengers? His "one good eye". At first, this sentence wouldn't seem to make a lot of sense, as only one of Fury's eyes is actually damaged, but The Reveal of this film makes it clear what he meant: After discovering that HYDRA had been operating inside SHIELD right under his nose, Fury didn't trust his own judgment, but he trusts Coulson's judgment without question. That is what makes Coulson his one good eye and that is why Fury went to such incredible lengths to bring him back, despite Coulson's pleas.
HYDRA's infiltration of SHIELD does have some real world historical parallels:
After the second World War, the United States and the Soviet Union really did recruit Nazi scientists. And why didn't people in the American intelligence community notice that the former HYDRA people were still being, well, HYDRA people? Because during the Cold War, American intelligence communities really were supporting right wing authoritarian dicators (who had some similar ideologies to the guy Captain America fought). American intelligence agencies really were highly suspicious of political activists marching for civil rights and against militant foreign policy (the F.B.I. director J. Edgar Hoover smeared Martin Luther King Jr., for example), and you can bet those groups would be high on the Helicarrier kill list.
Alternatively, Post World War 2 cooperation between the West and ex-Nazis and their fellow travelers went even farther. Many Eastern European ultranationalists who were willing to join Nazis to fight communism either became Western intelligence assets or found refuge in the West and took positions of influence themselves. This shows up in other media also (eg Alec Travelyan in James Bond film Golden Eye) but rarely are they shown to have gained positions of great power as in this movie.)
When Nick tells Steve the story of his grandfather, it just seems like two old men connecting over the past while killing time going down forty-plus stories in an elevator. It's really Nick's way of explaining why he does things the way he does and how he sees the purpose of Project Insight.
Cap's combat style is shown to be much more extensive in this movie. This is to be expected since it's his third outing, but it also has a story reason. In First Avenger, he was trained to fight as a normal soldier and had to develop his own techniques and find his limits. In Avengers, he was still fresh out of the ice and was mostly just shaking the sleep off. Now, he has been on several missions and has access to training facilities and techniques that allow him to reach his full potential. In the past, he was just trying to get to over that obstacle as fast as possible. Now, he can study parkour experts and learn their philosophies and methodologies.
The film's Darker and Edgier slant can also be illustrated through Steve's combat. In the first film, his shield was primarily used for defensive purposes, especially since he usually carried a sidearm. Here, his shield is his primary attack option; what was once a symbol that Steve was a defender now could be seen as Steve being an aggressor (although not so much that he would agree with Nick Fury on SHIELD's philosophy concerning future threats).
Here's an interesting thought, Captain America is on ice for 70 years and finds the world radically changed, feeling confused and missing out on history, now with The Reveal that HYDRA was the Big Bad of Marvel and SHIELD was compromised all through its history, the rest of the world feels somewhat similar to Steve, they've lived in a bubble and it burst. For Steve, that Bubble was Ice, for the rest of the world, it was the entire post-war period, meaning Steve and Present-Day Marvel are now aligned.
Given that in the chaos, no-one could tell who was or wasn't affiliated with HYDRA, SHIELD is kaput. But what about that flash drive? Zola's algorithm identified 700,000 people HYDRA considered such a threat to its goals that they were willing to kill them in broad daylight. In other words, the perfect replacements for SHIELD. And given how the algorithm targeted the President, isn't it likely that all the SHIELD agents who would have fought the new regime were on the kill list - thus identifying the loyalists? And Coulson is right at the top of that list.
Strucker was able to get a hold of Loki's scepter because it was confiscated by SHIELD. Perhaps HYDRA loyalists somehow got to the scepter before Thor could get his hands on it and it was declared destroyed.
A lot of people are upset Winter Soldier doesn't actually have that much of a speaking part when he's the Antagonist Title. Except...there's not really anyone there to speak. HYDRA hollowed him out so that he's an effectively mindless minion of theirs, a gun with no ability to act by himself. What did Zola call him? A fist of HYDRA, ie a hand completely under the control of and useless without the mind. Bucky doesn't speak because he doesn't have his own character any more - he's simply HYDRA's embodiment, their hand. The hand of an antagonist is not the limb you talk to.
Some have noted that Steve and Sam seem to form a loyal friendship awfully quickly for men who don't have much in common except being good guys and being ex-military. Then you remember Sam's story in one of their earliest conversations: he was part of a special-ops unit, went on a mission with his wingman, and had to helplessly watch as said wingman fell, literally and metaphorically. Sound familiar?
It may seem that placing the new Captain America exhibit in the National Air and Space Museum is a case of Mishmash Museum, but it's not as bad as it seems. First, NASM does cover everything aeronautical and astronautical — but a decent portion of its exhibit space is devoted to WWI and WWII aeronautics, both the European and Pacific theater (the former of which Cap and the Commandos served in, and presumably would have been mentioned in them). Second, there are usually at least one or two empty galleries in the Air and Space museum that are used for rotating exhibits (it has a very open floor plan and central corridor, and routinely handles the largest crowds on the Mall). And third (and most important), the National Museum of American History is currently in the middle of a full-building renovation, having started in 2002, with its second phase starting in 2012, way before filming started for Winter Soldier. Assuming that in the MCU, NMAH is also undergoing renovation, clearly they're refitting the space to accommodate a new Captain America/Howling Commandos gallery, and the one in Air and Space is the temporary exhibit!
Why would SHIELD need a set of helicarriers with enough weaponry to take down several thousand man-sized targets at once? Well, after the events of The Avengers, they've seen just what an invading alien army looks like: A horde. Not to mention the sizable guns on the deck, pointing at the sky. The Chitauri had a lot of light aircraft, and flying behemoths. Clearly, Fury was a big believer in not getting pinned in the same corner twice.
The real-life Winter Soldier Investigation was organized by American veterans returning from the Vietnam war, and its purpose was to publicly expose American war crimes and other abuses committed during the course of the war. Although the title is obviously taken from the comics run, it nevertheless is a depressingly strong parallel with Steve's relationship with SHIELD in the film.
The concept of the "Winter Soldier" also comes from Thomas Paine. His "Winter Soldier" is the one who goes through the whole grueling slog, long after the "Summertime Patriots" have given up the fight. It's a nice metaphor for Cap himself.
Combined with Agents of S.H.I.E.L.D., Coulson's resurrection is no longer a SHIELD secret due to the giant info dump. That's going to make for some interesting reunions.
Senator Stern was adamant that Stark hand over Iron Man technology back in Iron Man 2. Now that we see his real allegiances, no wonder he wanted his hands on those goodies.
Another one from Iron Man 2, but now we know why Howard Stark chose such an odd way to hide his tesseract research. If he wanted to hide something from Shield he had to hide it in a way that couldn't simply be cracked/hacked/or other wise collected by spies.
There's some serious brilliance in the fight scenes that show attention to even the smallest details when it came to making this movie, including the choreography. During his first fight with the Winter Soldier and his hit squad, Cap loses his shield early on and loses it again later when the Winter Soldier manages to force it away from him. On both occasions, Cap will still raise his arm as though he still had the shield when he's fighting or taking fire, showing how he's conditioned himself to use the shield in battle, even when he's aware that he doesn't have it at the moment. The Winter Soldier's fighting style also shows that incredible attention to detail, showing that the choreographers actually put some thought into the physics and logistics that having one of your arms be cybernetic would have in a close combat situation. The Winter Soldier's left arm isn't just stronger, it behaves subtly differently from his right, flesh and blood, arm. When he uses his knife, he uses it with his right hand because he can use it with greater speed and precision, but when he needs power, he braces the pommel with his left hand and you can actually hear the motors in his left arm winding up, basically kicking it into gear whenever he needs that extra boost of raw force.
For all of HYDRA's talk of wanting a world of order, there are several hints that it hasn't really let go of its Nazi origins or World War II. The mere fact that among Project Insight's targets include a good chunk of the U.S. Government and a sizable portion of New York City or that someone blatantly Nazi-esque like Von Strucker could rise up the organization's ranks, one can't help but wonder whether they're still following the Red Skull's shadow.
During The Avengers, it was mentioned that the Avengers Initiative had previously been shut down, which seemed kind of short-sighted in a world full of super-villains. Now that we know that HYDRA was secretly running SHIELD, it makes a lot more sense. And it also gives more reasons why Nick Fury basically defied the Council and brought the Avengers together, continuing to try to motivate them to come together as a team even while knowing full well that Tony Stark and Bruce Banner didn't trust SHIELD (or Fury himself). The Avengers double as Fury's answer to the old question of "who watches the watchmen"; don't forget that in The Avengers, it was SHIELD that launched a nuke at Manhattan, and the Avengers (alerted by Fury) who stopped SHIELD from destroying the city. And when SHIELD goes bad, Captain America and Black Widow - both Avengers - end up destroying the organization, because their loyalty to SHIELD is overridden by a greater duty.
Captain America and Black Widow were seen crossing a land border into New Jersey on their way to the abandoned Army base. Because New Jersey is a peninsula the only place such a land boarder is found is at the northern edge of the state where it touches Upstate New York. This might seem to be a mistake seeing as both of them would be coming from the Washington DC area to the south, but instead it makes perfect sense as bridges would be choke points that SHIELD could more easily monitor. Driving north then east through Pennsylvania on local roads would be more effective at evading SHIELD's manhunt.
In The Incredible Hulk, Banner when on the run emphasized the importance of not using items like credit cards or cell phones, since his pursuers could track him through those. That trip to New Jersey was pretty far so at some point Cap would have needed to buy gas. So how did he pay for it without his enemies tracking him? Unlike Banner, he had Black Widow with him, who wasn't currently on HYDRA's hunt list. Thus, her using her own credit card (or probably the card of her latest secret identity) wouldn't be an alarm to them; they'd just assume she was on another mission.
S.H.I.E.L.D is broken, Fury's faked his death, and their secrets just got uploaded to the Internet. As mentioned above, this includes Coulson. However, if S.H.I.E.L.D rebuilds, they're going to need a new director, one who is experienced, a good team manager, and completely immune to corruption. Phil Coulson would probably be very close to the top of that list. This one has been confirmed. The Agents of S.H.I.E.L.D. season 1 finale includes Fury naming Coulson the new director of SHIELD.
If you go back to the original Captain America: The First Avenger, there's a sudden blaring clue of Foreshadowing. After Steve is given the serum, and the celebration has started, everything goes to hell. Why? Because HYDRA had infiltrated their project. Infiltration was in their tactics literally from the get-go.
How did Zola go from being a mousy little guy ready to turn his back on Schmidt to become part of the Big Bad? Well, maybe he was always believed in HYDRA's ideas, but simply didn't like the way Schmidt was leading it. Given the chance to remold it in his own image, he seized it with both hands.
"Kate" didn't turn down Cap's offer to use his washing machine because she wasn't interested in getting to know him or because she already had a load running in the basement—she turned him down because she knew there was someone in his apartment and she needed to be prepared to provide backup if needed...as she did a few minutes later, when the Winter Soldier showed up.
Stephen Strange seems like a weird name for Sitwell to drop under the list of 'potential dangers', if we go with the assumption that he hasn't become Sorcerer Supreme yet - after all, the catalyst for his Origin Story is an accident that mangles his hands. Regardless of how good Zola's machine is, it seems unlikely that it would be able to predict something that random, or even that HYDRA would know enough about the existence and purpose of the Sorcerer Supreme to include it in their variables. Until you remember that Stephen Strange is a talented neurosurgeon, and HYDRA is awfully fond of brainwashing people; anyone with the potential skills to undo their hard work would probably make their hit list just for that. In fact, being a talented neurosurgeon would be an excellent reason for HYDRA to arrange the "accident" that mangles his hands. He can't surgically undo any brainwashing if he can't use his hands. With Project Insight shut down, they can't just blow him away from the comfort of a SHIELD Helicarrier anymore and killing him the up-close and personal way would draw Cap's attention, since Cap knows that Strange is on their threat list. Destroying his hands and dressing it up like an accident would take this threat off the table without alerting Cap. Perhaps we're looking at the Marvel Cinematic Universe version of his Origin Story? There is a Doctor Strange movie set for 2016.
If Steve is on Sam's left, then Sam is on Steve's right — Sam is Steve's right-hand man.
In The Avengers, Bruce Banner and Natasha note that each member of the team is on S.H.I.E.L.D.'s "threat watch", but only Cap is named in particular. Knowing that HYDRA has been running everything to do with S.H.I.E.L.D. since its founding back in 1946, it makes sense that The Star Spangled Man is considered a "global threat", as Tony put it.
It's not surprising that Steve has already seen WarGames, since in order to understand the repercussions of World War II, the first thing he'd want to do is learn as much about the Cold War as possible.
Fury tells Cap that his wife kicked him out when he shows up at his apartment after being attacked by Hydra. Cap realizes this is a lie, but it's not really. Fury was married to his job, and now SHIELD has turned on him.
When Cap gives his Rousing Speech and reveals to SHIELD that HYDRA has infiltrated them, it may seem implausible that so many would consider Steve's words; even if he IS Captain America, they might conclude he's just gone crazy and can no longer differentiate past from future. If, say, Earl E. Anderson announced that Nazis had infiltrated Congress, how many would believe him? But remember, this is S.H.I.E.L.D. that's hearing his speech. They've discovered that the Norse gods are real and witnessed an alien army come to Earth through a portal from space. And Agents of S.H.I.E.L.D. demonstrates that it's basically their job to uncover and handle a ton of weirdness every week. HYDRA being active again is possibly nowhere near as crazy for them to believe.
Steve taking his WWII suits has at least two themes going for it; one, is a symbolic that the same oldCaptain America is finally going to back against HYDRA again, to save the world, just like what he did before he got frozen. Two, the pragmatic reason, if he got lucky, he could makes The Winter Soldier remember him again, however small chance it got (if you remember, in The First Avenger Bucky is the one who jokingly suggest him using suits based on his show costume). It can also have connotations that Steve is shedding his loyalty to corrupted SHIELD (which provides him with suits he wore in the beginning) and return to his old war hero persona.
If you think about it, Sam's jetpack power was kinda overkill, since it could support weight both Sam andSteve with almost no trouble, barring Sam's trouble with Steve's weight. However, if you think about it, it makes perfect sense. Sam's job before he retired are basically Combat Medic for people Trapped Behind Enemy Lines, which can included evacuation. So of course the jetpack should be designed to be able to bring another soldier, most likely injured, and maneuverable enough to evade big guns that can one-shots them.
If you look at the targets of Project Insight you realize something: even though it was targeting big names like Banner and Stark, as well as the loyal SHIELD agents, it was also targeting POTENTIAL threats, otherwise regular people with a certain mental and emotional makeup that proved to be against HYDRA's interests. The brilliance is who they are up against. Remember, Steve was just a skinny kid from Depression-era Brooklyn. He was probably the last person anyone thought would end being a world-saving hero three times over, least of all himself. HYDRA learned from Captain America himself that you can't underestimate the potential of even one human. They were trying to prevent another Steve Rogers.
Cap is the perfect person to stop HYDRA-infested SHIELD. How? He is the only member of SHIELD to NOT grow up under the cynicism and fear they created through their machinations. If he had, he would probably been just as susceptible to their plans as everyone else. Hell, probably the main reason why Nick Fury revealed Project Insight to Cap was because he knew Cap would be the only person who couldn't justify it, since he never lived through the kind of world where Insight actually sounded like a GOOD idea. This also means that his being frozen for years, while devastating emotionally, was probably the best thing to happen to the world, because he wouldn't be who he was, and did what he did, if it hadn't happened.
With the revelation that SHIELD had been compromised by HYDRA, the in-universe reason for the lack of army involvement in The Avengers, becomes clear. It's because their intelligence, and entire chain of command had been rigged and compromised from the beginning. The National Guard would be close enough to move in on their own (which HYDRA couldn't prevent without looking extremely suspicious), but it would have been easy to keep the rest of the military from mobilizing in time. Remember, armies can only work with government sanction. And when said government got their intelligence from SHIELD, corrupted by HYDRA...yeah.
The reason Maria Hill urges Natasha to finish her mourning over Fury's "corpse" isn't because she has places to be and people to answer to, it's because she either has to get him out of there before he wakes up and ruins the cover, and/or there are counter-meds she has to administer within a certain time frame to save him.
You know that "On your left" scenes in the beginning? It nicely shows Steve's Character Development since The Avengers. In Captain America: The First Avenger, Steve is mostly polite, but honest to the point of bluntness, and only shows his (rather dry) sense of humor with friends and people he's comfortable with. In The Avengers, Steve is still politely honest, but distant and clearly still reeling from finding himself 70 years in the future. He barely smiles, let alone jokes around the way he does with Bucky. In this movie, we not only see Cap being sarcastic without being mean, he also (politely) flaunts his Super Soldier abilities by lapping Sam several times.
Sam's comment "I do whatever he does... just slower" is funny enough, but it becomes heartwarming when you realize it fits Steve Rogers' condition pre-serum. Even when he physically outmatched by everyone during his boot camp, he just didn't give up.
HYDRA existing within S.H.I.E.L.D. actually makes sense.
In Captain America: The First Avenger, HYDRA is making weapons using the Tesseract. In The Avengers, Steve finds HYDRA weapons on the hellicarrier, and Tony turns up plans for new Tesseract-powered weapons.
In The Avengers, Tony’s program that’s meant to reveal “every dirty secret S.H.I.E.L.D. has been trying to hide” initially fails, implying greater security than Tony expected and that all files with information about HYDRA have security no one else in S.H.I.E.L.D. knows about. In Captain America: The Winter Soldier, Fury tries to access files that have security he doesn’t even know about, most likely due to HYDRA-related information on them.
In The Avengers, Tony compares Fury’s justification for the Tesseract-powered weapons to a “nuclear deterrent”. Even before HYDRA is revealed in Captain America: The Winter Soldier, Steve says, “This isn’t freedom, this is fear,” regarding Project Insight. Sounds a bit like a nuclear deterrent…
The largest of HYDRA’s Tesseract-powered weapons is the Valkyrie, a giant aircraft with heavy weaponry that can cause countless deaths around the world in mere hours (it could wipe out the Eastern Seaboard in an hour, and Schmidt’s target is everywhere.) By Captain America: The Winter Soldier, The Tesseract is back on Asgard, but S.H.I.E.L.D. has built three giant aircraft with heavy weaponry that can cause countless deaths around the world in mere minutes. The Insight hellicarriers are modern-day Valkyries on massive steroids.
During the assassination attempt on Fury, it can seem like a coincidence that Winter Soldier was waiting for him the very same block he managed to turn and escape to. But in fact, that wasn't a coincidence at all, but a Batman Gambit. When Fury tells his car to find him an escape route, it responds that the streets ahead are blocked, with one still clear. Fury takes its advice and plows through the crowded street in order to reach the clear one... just as Winter Soldier expected.
Look at the SHIELD insignia on the flight decks of the Insight helicarriers. They're red, like the Hydra sigil.
When Winter Soldier is being prepped by Pierce, Pierce tries to make what they're about to do sound like a good, heroic deed he should be proud of, specifically trying to make it sound like if he doesn't do this, the world will be plunged into chaos. While it doubles as propaganda, there's a deeper meaning. to get him to do what he wants, he had to convince him that it was a heroic deed. In other words, behind the brutal and silent combat style, the scary mask, and the hyper-lethal skillset, at his core, he's still a good man thinking he's doing the right thing. While he's brainwashed, he's still a moral human being trying to be ultimately a good person, and thus, means that Bucky really is still inside. What's more, in the final fight with Cap, he opts to not finish Steve off once Steve stops fighting, and then saves his life as he starts remembering who Steve is, meaning that even if he's willing to do all those awful things, he's still incapable of killing a man who's surrendered and trying to make peace.
It's been conjectured that one of the reasons Steve chose to wear his vintage suit was to jog Bucky's memory of him. It doesn't initially work; the Winter Soldier fights him. It's not until Steve removes his mask, drops his shield, and starts talking to Bucky about their lives together that the Winter Soldier really starts to crack— because Bucky Barnes was the one guy who never saw "Captain America" when he looked at Steve. Bucky wasn't following Captain America, Bucky was following "that little guy from Brooklyn" to the end of the line.
It was essential that all of SHIELD had to be destroyed in order to destroy HYDRA. The HYDRA slogan is "cut off one head, two more take its place". If you can't attack the head, what do you do? Attack the body. HYDRA was a parasite in SHIELD, so it had to burned to the ground to be saved.
Going across multiple films, shorts and the TV series, Sitwell was a good friend of Coulson's. Simmons flirted with him to try and get into a restricted area for information. And the entire time, he was a HYDRA mole, and no one who knew him suspected. At all.
Yay, we took down the corrupt government agency it turned out that SHIELD was! Happy endings for all! You know, except the hundreds, maybe even thousands of non-HYDRA-affiliated employees who are now not only out of a job, but now have an organisation that turned out to be mostly run by Fascists down as their last place of employment. In Agents of S.H.I.E.L.D., Coulson makes it pretty clear that if you want to be part of SHIELD, you have to give up hopes for any real normal life. So there's now a LOT of ex-SHIELD agents who sacrificed almost everything for SHIELD, and might not be able to find work anywhere else. That's a lot of people who could be a little resentful. What's to bet at least one ends up either as a villain or a villain's minion?
On the flip side, what happens when you're a morally upright SHIELD agent who discovers that they unwittingly helped further a plot to kill literally millions of people? You can bet that those people are going to need some serious therapy. Not just the Aircarrier plot - how many SHIELD agents do you think are going to be looking back on any mission that didn't quite feel right, but that they were convinced was for "the greater good"?
Political thrillers always end up being topical whether they intend it or not. Thousands of ordinary working people, who had no part in their superiors' wrongdoing, losing their livelihoods because of the directors' sins certainly seems topical at the moment.
Not only that, as shown on Agents of S.H.I.E.L.D., many of the loyal S.H.I.E.L.D. agents had no idea who was HYDRA and who was on the up-and-up. How many loyal agents were frightened/tricked into fighting and killing other good agents by HYDRA's machinations?
Also, with S.H.I.E.L.D. now labeled a terrorist organization, all remaining agents are being hunted down by world governments whether S.H.I.E.L.D. loyalists or HYDRA sleepers.
It is actually worse. It is implied that Black Widow dumped EVERYTHING onto the internet. Possibly including personnel records. Did loyal SHIELD agents infiltrate the Ten Rings? The Ten Rings now know about about him. Did a SHIELD agent kill a Russian mobster on an op out of necessity? The Russian mob knows where he and his family lives.
In a slightly more optimistic point, generally law enforcement agencies delete files relating to covert assets when they go undercover. While their past alias' and names will be still recorded, their photos will be erased and the only people who'll know they're undercover would be their handlers. So, undercover agents? Should be safe for now, they just don't have an extraction plan anymore. As for their families, local police and the FBI are likely to mobilize faster than criminal organizations, so they'd probably be put into Witness Protection before anyone can get to them.
SHIELD's collection and continued work on HYDRA weapons in The Avengers both makes more sense and seems a lot more ominous now, doesn't it?
Further than that: since HYDRA never lost control of the Tesseract (until The Avengers, anyway,) who's to say they hadn't spent seventy years trying to bring their old leader back from the depths of space? Maybe that's what Project Pegasus was really created for, what with the convenient landing pad and all...
And on top of that: not only was SHIELD's Phase 2 in the hands of HYDRA the whole time... but so was the Destroyer's Asgardian technology. And if the DVD shorts mean anything, Chitauri tech as well. And Stark's repulsor tech (which might have even included Arc Reactors). Really, HYDRA can potentially have control over every advanced tech ever seen in an MCU film.
What's more, by the end of the movie, every last scrap of that information, S.H.I.E.L.D.'s and Hydra's, is now online for literally anybody at all to use.
It's not so much Fridge Brilliance as text in the movie but SHIELD has more or less replaced the CIA, Department of Homeland Security, and probably some branches of the FBI. The Senator isn't kidding when he mentions they've crippled the USA's intelligence apparatus. SHIELD must have had a budget in the hundreds of billions which has all gone up in smoke. On top of that, SHIELD was multinational. It answered to the World Security Council, not the JCS. Agents of S.H.I.E.L.D. operated globally.EVERY NATION FELT THAT HIT.
Related to the above; when Pierce sees the Project Insight helicarriers start to go down in flames, he doesn't have a Villainous Breakdown, he just sighs belatedly and says, "What a waste." For SHIELD, it was the Fall of the Bastille. For every nation in the world, it was September Eleventh meets Scandalgate. For HYDRA, it was their first setback in seventy years - the equivalent of a very successful corporation being forced to recall a product. The Avengers are going to have their work cut out for them.
Captain America's distaste for the machines becomes a clever bit of satire when he is not offended by the Drone-Hellicarriers because he's afraid of some sort of Skynet-esque uprising. No, he's upset with the fact that if SHIELD starts "proactively" hunting down targets then it crosses the line to murder. The thing is, due to SHIELD's research, it is INCREDIBLY EASY to compile a list of names of people needing to die and if it hadn't been in America—they probably wouldn't have cared. Perhaps the scariest bit is the fact that of the 700,000 they wanted to eliminate—it's implied everyone else would have capitulated. Worse, this is backed up by hard data.
Another bit of Fridge Horror isn't that Zola rebuilt Hydra in SHIELD. It's that Zola found enough sympathetic ears to rebuild a Nazi-esque organization out for world domination in the heart of the world's intelligence arm. Possible Fridge Brilliance there. Zola is smart enough to write an algorithm that can calculate anyone who will be some sort of threat to HYDRA. Who's to say he couldn't write a similar one to find people most susceptible to HYDRA's way of thinking?
Assume Cap had failed, or at least had failed to shut down the helicarriers before they were fully operational for about thirty seconds. Even setting aside all the people who died, presumably the highest-threat targets would be hit first—Tony, Rhodey, any other superhumans. One of those targets would have to be Bruce Banner. But it's implied in Avengers that even if Banner sustains lethal injuries, the Other Guy will appear, completely unharmed and out for blood. Now plug that in—odds are Bruce might have been with Tony, working on some project or another, and then suddenly he's grievously injured and his closest friend is dead. How angry would the Hulk be?
Howard Stark was murdered by HYDRA apparently because he figured out that they were infiltrating SHIELD. If he knew he was being targeted, he may have deliberately sent Tony off to boarding school/kept his distance in order to keep Tony safe. If he knew of HYDRA's terrifyingly deep level of infiltration, that would explain why he had to hide the details of his newfound elements in such a contrived manner, in order to protect it from falling in the wrong hands. He knew that only his son would be not just smart enough, but also a lateral thinker and would notice it sooner or later.
Zola's algorithm itself is an interesting meta example. It uses all the digital information found by what is essentially the whole planet's CIA to estimate who is going to grow up to be exceptional. This would include the pedestrian stuff like scientists, politicians, civil and military leaders etc. But we see heroes tagged in there as well. Zola's algorithm, in that case, could act as an Origin Story predictor.
Natasha releases all of SHIELD and HYDRA's information without anything being removed or censored. How many genuinely good agents who, like Natasha and Fury, believed they were working to protect people were murdered as a result of their operations and locations being put on the internet? Especially deep cover agents or ones in hiding? As Coulson points on in Agents of SHIELD, there's also a legitimate reason as to why certain bits of information are kept secret, like otherworldly artifacts, alien technologies or generally anything that would be bad news for the world if it fell into the wrong hands.
While Fury's story about his grandfather is pretty awesome because he's able to intimidate tons of thugs into backing of by showing them he's packing, keep in mind that during the time period, if he hadn't been packing he might have gotten killed.
HYDRA's absolute faith in Zola's 'future-predicting' machine is horrifying in itself. Considering how many variables exist in life, and how impossible it would be to account for every potential change and how it would precisely effect every single person at every point in their lives in the whole entire world regardless of how detailed your information on their past is, it's very likely that, even if you take HYDRA's Well-Intentioned Extremist tendencies in the most sympathetic light possible, they are still putting their faith in a system that is very unlikely to accomplish anything like 'peace', and killing millions of people for nothing.
The Winter Soldier is supposed to be the stealthiest, deadliest and most efficient assassin in the world. So why the hell does HYDRA have him attacking his targets in broad daylight, carrying guns with heavy firepower and being as unstealthy as possible even before his climactic battle with Captain America aboard the third Helicarrier? Because they never intended for him to survive his final mission. After all, what would be the need for an assassin if the world was going to be at peace? At best, they expected Bucky to go down in a hail of bullets or be decapitated with a well-aimed Cap Shield, or die in the Helicarrier crash. At worst, they were going to kill him once he returned back to headquarters. Or even worse, put him on ice indefinitely. Either that, or they wanted a very public couple of incidents right before they kick off their final plan, in order to cause more panic.
Strucker now has his hands on Loki's scepter, a mind-controlling weapon, Reality Warper Wanda Maximoff, and her could-kill-you-in-the-blink-of-an-eye brother Pietro. Put 2 and 2 together...
Black Widow and Fury released SHIELD's/Hydra's entire secret archive to the public BEFORE Captain America and Falcon were able to destroy the helicarriers and stop Project Insight. Assuming that the helicarriers select targets for elimination using Zola's algorithm in real-time, then that move would have resulted in greatly increasing the amount of deaths since many more people who would have otherwise submitted to Hydra's rule will resist instead after learning about all the atrocities that they have commited in the past and how they have been manipulating historical events for the past 70 years.
A lot of people may or may not have missed it, but when Steve sees Carter, it almost certainly isn't the first time he's seen her forget who she is.