These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Harsher in Hindsight: Church and Carolina's decision not to say goodbye at the end of season ten to make it so they're "just not here right now" was initially portrayed as heartwarming, but it turns out Tucker and Caboose are both hurt by Church's disappearance.
Awesome Ego: Felix. He's got a bit of an ego, but there's no denying he's badass and many fans love him. The fact that he's actually an evil bastard working with Locus to kill the population of Chorus does little to minimize this.
Badass Decay: While Carolina's reappearance is a Big Damn Heroes moment, her performance is much less impressive than what fans are used to seeing from her (this may partially be due to Special Effect Failure causing her fight to seem clunky), and she gets stabbed in the leg by Felix, severely hindering her fighting ability for the rest of the season. The next episode has her have a bit of difficulty with a trio of unnamed mooks. A Justified Trope, since she has been havingBad Dreams about Sigma.
Base Breaker: Felix; many fans think he's a Mary Sue, others find him fun and entertaining. It depends on how you feel about the most badass member of the Resistance being voiced by the writer of the season, who would, by extension, be responsible for the perceived badassery of him. Considering Episode 10,this may have been intentional.
Broken Aesop: When listing off what they can do without Church/Epsilon in Episode 7, the crew lists off the defeat of C.T. and The Meta among them. Except... C.T. was about to kill Tucker when Epsilon floated up and killed C.T. directly. So, they didn't do that without his help.
Of course, Tucker did manage to keep the entire raiding party from getting into the temple for months, in a display so badass he was apparently enough of a threat C.T. had a severe Oh, Crap the second the temple doors opened.
Cargo Ship: Felix x Money is a popular one within the fanbase, particularly after it was revealed that Felix was willing to drop a nuke on civilians if it meant he could get money out of it.
Every named lieutenant in the New Republic army got instantly popular after the first episode. The most popular by far seems to be Jensen; being the first prominent female character who wasn't constantly pissed (besides Sheila/FILSS and Sister, at least, and not counting Kimball who was introduced first but her characterization wasn't clear until after Jensen), being incredibly Adorkable, and voiced by a popular Rooster Teeth personality all probably help with that.
On the flip side we have Emily Grey who's with the Federal Army of Chorus who is already steadily gaining popularity. Doyle seems to be exempt from this, though.
Evil Is Cool: Locus, once more, but also Felix, whose reveal as a villain suddenly caused his popularity to skyrocket.
In the trailer, Tucker's response to Kimball wondering how they'll win the war if they can't even rescue a few prisoners is, "We'll wing it." His attempts at winging it in his first mission end up getting most of his men killed.
Tucker leaves Pamolo as a look-out because he believes having him on the field will get everyone killed, an assessment Pamolo agrees with. By episode's end, Tucker's deviation from the plan has led to the deaths of his other two men.
Every interaction with Felix prior to episode 10 now that he's revealed to be a bad guy. Felix's friendly antics in Season 11, even going so far to take a bullet for the team? Turns out he was just playing them, pretending to be on their side to gather intel for his employers. His efforts to make Tucker a better soldier and leader also take on a darker turn when it's revealed he never believed in the rebels' position and was working with Locus the whole time.
Control is actually the Chairman, who is also the CEO of Charon Industries, the "Insurrection" fought in seasons 9 and 10. After that reveal, it makes you question every action he does in the series, but especially his conversations with the Director and sending Wash to find the Epsilon unit.
Les Yay: Doctor Grey calling Carolina "sweetie" and very...eagerly offering to psychoanalyze her.
Love to Hate: Felix, after episode 10. Though he is a sociopathic, hypocritical, jerkass of a villain, it's hard not to admire how manipulative he is.
Their boss, Control, is the one giving them the commands in the first place. In episode 12, they tell Locus and Felix to take advantage of the situation that the Reds and Blues are missing and report their deaths to escalate the conflict on Chorus. It later turns out that he's really Malcolm Hargrove, aka the Chairman.
Felix crosses it when it is revealed that he and Locus had stirred up the Civil War on the planet Chorus to kill everyone on the planet. Not only that, while his boss, Control, (or at least whatever third party Control is a part of) wants everyone on Chorus dead to get the alien technology on the planet, Felix seems to go along purely just so he can kill people, even saying he would rather nuke the planet from orbit than start a Civil War. Plus his psychopathic tendencies, Felix makes Locus look tame in comparison.
For the Evulz motivation confirmed in episode 18 when he brags that the feeling that he's outsmarted both sides means more to the psychopath than any amount of money.
Control would appear to have crossed it from the very beginning, considering his plan involves killing off an entire population, but The Reveal that his identity is Malcolm Hargrove, aka the Chairman, makes this worse when you take his prior actions into account.
One-Scene Wonder: The 'Why Snowman?' guy is super popular with a lot of the fandom.
Special Effects Failure: This season's fight scenes weren't animated by Monty like they used to be, with two different animators taking over and using a different programming than Monty. Thus, the CGI is more jarring than usual.
Carolina vs Felix was a bit clunky, compared to the amazing fist fights seen in their Halo 3 model CG. It seems possible this particular scene was added last minute, since all of Felix's actions during his rant were incredibly smooth.
In the following episode, Carolina's Halo 3 model shows some rather jarring shading and texture issues, especially when contrasted by the excellent models of the security troopers she fights.
The scene where Wash gives Caboose Freckles back really sticks out from the scenes immediately before and after it.
Uncanny Valley: The Chairman hasn't gotten much love for his full body model. Apparently, his model was done at the last minute, which might explain this.