Alas, Poor Scrappy: Emmett in the Season 3 opener. An Asshole Victim for sure, and there are many who would quickly say that he deserved what he got, but others think it was a bit shocking given that, by and large, the Buy More crew was a separate world from the the Spy world and any danger to them was usually done for slapstick. The flippant way Casey covered it up while pressing the Reset Button was a bit callous, even for him.
Ellie got over Chuck ruining her wedding pretty quickly. This is a Justified Trope, as Chuck fixed her wedding rather quickly, and gave her the wedding she actually wanted, as opposed to the original, which was what her mother-in-law-to-be had arranged.
Viciously subverted by Shaw seemingly getting over the reveal that Sarah killed his wife. Not so much.
On the other hand, it also gave us the relief of finally bringing the rest of the main cast in on Chuck's secret.
Fans grew tired of the Ring, as the reduced episode count meant that the show simply didn't have time for any standalone episodes, and the entire season, aside from two episodes, featured them as the villains of the episode; and the two episodes where they aren't villains still feature the Ring as a threat.
In later seasons, if a certain skill is needed, it's probably in the Intersect. Possibly one of the few times where this trope is actually justified by the mythos.
Some fans view the reveal of Casey's backstory in season 3 as this, as much of it (particularly his age, but also several direct contradictions in how long he has served under Beckman) doesn't mesh with any previous details we learned about him.
The late season 3 plot with the Intersect slowly destroying Chuck's brain, since it literally comes out of nowhere and the characters treat it as if it had been going on for some time. The problem is largely down to NBC's decision to order an additional 6 episodes for the season, as the show was in production for the intended season (And potential series) finale when the decision was made. Subsequently, the writers had to write another 6 episodes in a story arc that had already reached it's conclusion, and the plot point couldn't really be introduced in the first two of the six episodes without putting a damper on Chuck and Sarah's relationship, as those episodes directly dealt with the ramifications of them becoming a spy couple.
The reveal halfway through season 5 that Clyde Decker was being blackmailed into trying to bring down the team by Shaw. Richard Burgi's performance never once gave any sign that his motivations were anything but his own.
Broken Base: The comparative quality of Seasons 2 & 3 is a point of contention among the fans. Inarguably however, the budget cuts that impacted on the visual effects & the removal of Anna's character just to save money on actor salaries was not well received.
Crazy Awesome: Casey, Morgan and Steve Bartowski. Then there's Alexei Volkoff, who's just something else entirely, both in terms of being completely crazy and equally awesome.
Pretty much everything the series shows about the various intelligence agencies it features is wrong. Neither the CIA nor the NSA has any law enforcement authority; in fact, the NSA doesn't even have field operatives and would not recruit them from paramilitary black ops teams if it did. Instead, they share their data with actual law enforcement, which then goes in to make the arrest. The idea of a rivalry between the CIA and NSA, featured in the first few episodes and presented as the reason the Intersect computer was repurposed in the first place (the CIA and NSA were ordered to "play nice"), makes very little sense, as the two agencies handle very different fields: the CIA gathers HUMINT (intelligence from living sources), and the NSA gathers SIGINT (intelligence from signals, including but not limited to emails, digital surveillance, and wiretapping). For comparison, the two agencies competing would be like an electronics store and a diner trying to drive each other out of business. The CIA is forbidden to operate within US borders, but nearly all the missions Chuck and co. undertake are local. CIA operatives are actually called officers, CIA agents being native civilians who are cooperating with an officer, but Sarah is always referred to as Agent Walker instead of Officer Walker. Still, the show would not be nearly as entertaining if these agencies were handled realistically.
In "Chuck Versus the Muuurder" Chuck mentions that Lewis' World of Warcraft guild, "...brought down Deathwing, world first." However the episode aired eight months (almost to the day) before Deathwing was even killable. Most of the show's target demographic would have known this when the show aired.
"Chuck Vs. Tom Saywer'' said that Atari was a Japanese company; it was actually American, and was ironically owned by Warner Bros.' parent, Warner Communications, from 1976 to 1984.
Die for Our Ship: Bryce Larkin, and quite honestly, anyone else who comes between Chuck and Sarah.
Carina was so popular after her first appearance that she later made return appearances in the third season episode "Chuck Versus the Three Words" and the fourth season episodes "Chuck Versus the CAT Squad" and "Chuck Versus the Cliffhanger".
The Director is quite popular among the fandom, despite only appearing in a handful of scenes in two episodes.
Cole Barker, while not a very prominent character, easily steals the episodes he's in thanks to being a charismatic, badass, and loyalJerk with a Heart of Gold. Being part of MI-6 and a heroic British character after initially appearing to be a typical Evil Brit also help that. His graceful acceptance of Sarah's rejection also certainly did not hurt with the Chuck/Sarah shippers, handily averting Die for Our Ship.
Fulcrum agent Tommy, despite only appearing in the episode which first introduced Fulcrum (and briefly in the one before it), is quite popular among the fans.
Ellie's then-boyfriend, now-husband, Captain Awesome, was suppose to be revealed as an enemy spy for Fulcrum at the end of the first season. However, he became this, and his character was rewritten to a genuine Nice Guy.
Epileptic Trees: Everyone knows that Stephen Bartowski is Orion. Bryce also mentions that he befriended Chuck in college because he owed Orion a favor. Since Bryce is responsible for Chuck receiving the Intersect, is Orion the one really behind that part of the plot? Yeah, he denies it... but it seems HIGHLY SUSPICIOUS.
Some fans definitely like the idea of Carina/Morgan. It also helps that she too has definitely warmed up to him, but alas, Morgan chose Alex over Carina and Anna.
Many fans preferred Anna with Morgan over Alex.
Despite being happily married to Captain Awesome, the fans tend to frequently ship Casey and Ellie.
"Funny Aneurysm" Moment: "Chuck Vs. the Third Dimension" has a scene where the rock star played by Dominic Monaghan is dedicating his upcoming concert in Nelson Mandela's memory, the joke being that Monaghan's character was oblivious to the fact that Mandela was still alive. However, it's a lot less funny after Mandela actually passed away in December 2013.
Growing the Beard: The second season is a nice step above the entertaining but uneven first season. This could partly be down to it getting cut short by the writer's strike.
Nicole Ritchie's performance got this surprised reaction from many viewers.
Brandon Routh's performance as Daniel Shaw initially received numerous criticisms over Shaw being The Stoic to an unbelievable degree. Once Shaw's FaceHeel Turn happened, Routh's portrayal became a lot more charismatic as Shaw became a Magnificent Bastard; winning over critics of his performance in the first half of the season and his earlier turn as the title character in Superman Returns.
Chuck's throwaway line to Ellie in the pilot that he'll get to work on a five year plan the next day. At the time, that's just plain funny because the next day he meets Sarah. It becomes Hilarious In Hindsight because the show ended after its fifth season.
Chuck's comment to Sarah, after she gives him a faked photograph of the two at Comic Con dressed as Han Solo and Slave!Leia in "Chuck Versus the Sand Worm", that they've never actually been to Comic Con. Over the next few years, the Chuck panels at Comic Con would go on to be considered highlights of the event.
The first season featured Bryce Larkin engaging in a bit of Super Dickery, as he got Chuck kicked out of Stanford to protect him from being recruited into the CIA against his will. Matthew Bomer was not only a contender for playing the role of the the poster child for Super Dickery, but would go on to voice him in an animated film six years later. And who got the role of Superman over Mr. Bomer? Brandon Routh, who would join Chuck as Daniel Shaw in the third season.
Casey displays his Osama Bin Laden targets in an episode that aired one day after Bin Laden was killed.
On the subject of DC Comics castings, Zachary Levi himself went on to play Shazam, with his role existing in the DC Extended Universe, while Routh's role is a part of the Arrowverse. Given the Fandom Rivalry between the twonote due to characters from the latter often being either Exiled from Continuity or killed off when they appear on the former since the films take higher priority, much to the chagrin of Arrowverse fans., having Levi and Routh playing arch enemies can feel like the rivalries between the two DC media franchises personified.
Additionally, Chuck and Shaw's rematch in the final season featured a cameo appearance from Stan Lee in the episode. Given how both actors have now prominently gone on to play DC heroes (again in Routh's case), it feels like him showing up for the other team. Taking that into account it feels prophetic about his appearance in Teen Titans Go! To the Movies where he comments about loving cameos so much he even makes them for the Distinguished Competition.
We now know that Casey's super-Republican gun nut personality is not an exaggeration in the slightest of Adam Baldwin's real political beliefs.
Due to Adam Baldwin's controversial comments on gay marriage, Chuck kissing Casey can be seen as either this or "Funny Aneurysm" Moment, depending how you view things.
Morgan towards Chuck, but he grows out of it (Mostly) as the series goes on and he undergoes some Character Development by becoming less dependant on Chuck.
Casey and Morgan gets lots of this after Morgan becomes a member of Team Bartowski in season 3. They even move in together in season 4.
Casey: You know, half of marriages end up in divorces. (Casey and Morgan drink juice at the same time) Chuck: It's nice to see yours is going so well.
Informed Wrongness: We're supposed to agree with Sarah in "Chuck vs the Helicopter" that Chuck was at fault for their mission going array, since he didn't trust her. Of course, the only reason Chuck didn't trust Sarah was the explosive that went off in Casey's car, and had Casey and Sarah trusted each other as they were supposed to, the mission would have worked ut fine
Love to Hate: Both Shaw and Volkoff are the show's most iconic villains for very good reasons. Shaw for his charisma and intellect as well being the most despicable badguy on the show making him just fun to hate because of it. Volkoff for being a delicious mix of being fun, goofy, hilarious along with being insane and ruthless at the same time.
Shaw trying to kill Sarah was his Start of Darkness. He crossed the MEH when he shoots Stephen Bartowski in order to cause Chuck enough emotional pain he'd be unable to flash and fight him head on.
On a slightly less severe one, Emmett secures his place as the most hatable man on the show (who isn't a criminal) when he manipulates Morgan into getting evidence of Big Mike's laziness to get him demoted so Emmett can take the store manager position. Its made worse by the fact that, not only did this involve abusing the trust Mike had in Morgan, but also the trust Mike had in Emmett himself. Given his general personality, this act shows that Emmett might actually be a complete sociopath.
Daniel Shaw. Some fans saw him as a knockoff of Bryce Larkin written in to cover Matt Bomer leaving to do White Collar, and not much else. Brandon Routh had virtually no chemistry with the rest of the cast and was The Stoic to an extent in broke Willing Suspension of Disbelief. At least until his FaceHeel Turn, when Routh proved that no, he's not actually a robot.
The Ring was often viewed as this, with many fans finding them not nearly as interesting as Fulcrum. This was exacerbated by Fulcrum's complete disappearance after Season 2, and that every episode of Season 3 directly involved the Ring, leading to severe Arc Fatigue (whereas Season 2 mixed standalone episodes with the Fulcrum arc plot). It gets a lampshade in the final episode of the series when a Fulcrum agent from Season 2 reappears in a cameo with Quinn, and disgustedly dismisses the Ring as amateurs.
Seasonal Rot: Fandom was split over whether season 3 was worse than season 2, but most agree that the fourth season isn't as fresh as the preceding two.
At the end of Season 3, Chuck receives his "inheritance" from his father - Orion's spy bunker located underneath the Bartowski's former family home. This is used to introduce one plot point (Chuck's mother is missing because she, like her husband, is involved in the spy business) before being destroyed, despite the potential to use it to introduce several more plot lines in future episodes.
The Season 4 winter finale teased us with Ellie getting the Intersect after Chuck lost it. Nope, just a Red Herring.
We never do learn just who it was Sarah's dad conned that led to Graham arresting him to protect him.
Vindicated by History: Chuck was one of the first shows where the fans were able to take advantage of social media to facilitate "Save our show!" campaigns, and did so with such efficency that the only time they ever actually campaigned for a renewal was after season two, with every season following featuring fan campaigns on Twitter during the season to show NBC and the show's sponsors that there was an audience watching the show, regardless of what Nielsen ratings showed, which led to NBC renewing the show for it's fourth and fifth seasons before the fans actively mounted a campaign for a renewal. To this day, the cast and crew actively credit the show's fandom with keeping Chuck on the air for 5 seasons, and the model Chuck fans used has since been utilised by other fandoms since then.
Wangst: While not as guilty as other shows, the writers do tend to hit the "Chuck and Sarah can never be" chord a LOT. Until, of course, they are; then the writers keep going to the "Chuck and Sarah have an issue but choose not to talk about it" plots.