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.
Given the large number of variations on the same stories, there's quite a bit of this within the spinoff comics as well. One of the more common interpretations in runs of the first gen and its remakes is the common Fanon theory of Blue/Gary being Oak's Unfavorite while his grandfather favors the MC appears quite often. Other runs paint him as a flat-out Jerkass, while others split the difference for a Jerkass Woobie.
Another frequent point of variation: how gym leaders and other trainers respond to death on the battlefield. Any given gym leader could be portrayed as a professional who has accepted death as a natural consequence of battle, a friendly foe who's honestly shocked at seeing their opponent's pokemon die, or an utter Jerkass who gloats and rubs the loss in their face.
Complacent Gaming Syndrome: Plagued with it to a degree. Despite the random nature of the game and how death can result in some odd teams, a lot of the comic makers tend to make similar choices of starter Pokemon and likely make similar choices on keeping mons if they are able to use them. A Johto locke that picks Chikorita tends up attract intrigue and curiosity since it is a rare occurrence while a Sinnoh locke that picks a Chimchar is regarded as another run-of-the-mill Nuzlocke.
to derp: to catch an Idiot Ball, especially killing a teammate as a result
Mary Sue: One of the biggest complains about nuzlocke comics (as a genre) is the main character turning into this.
For instance, the anomaly-like ability to completely understand and communicate with their Pokemon is rather common to see in many Nuzlockes despite the fact only a single known person, N, has it in the Pokemon universe. It doesn't help some of the sue traits are the result of good fortune on their Nuzlocke run, the game's plot deliberately revolving around the player character, the real life savviness of the artist being able to avoid most deaths through means of exploiting the Rock-Paper-Scissors. In a way, the character coming off as a sue is justified since it is less of an issue of bad writing and more of the way the game is designed.
Some of the better runs have been deconstructing this, though. Along with the aformentioned upgrade to Plasma's legitimacy, there's also leadups to the NPCs (mostly rivals) feeling worthless next to the protagonists, and ocassionally Pokemon turning into Death Seekers for whatever reason.
A LOT of Nuzlockers seem to have waifu-time with their favorite Gym Leaders. Or, more recently, with N. Here's actually a few Nuzlockers who shipped rivals with Gym Leaders.
"Stop Having Fun" Guys: It is to be expected, given it is part of the Pokemon fandom, albeit rare. There are some who take the challenge rather seriously and will criticize the teambuilding of other players (if they are sharing the progress and results of their challenge) even though one of the premises of the challenge involves adapting to having no choice on what mons you can use outside of ones given as gifts.
Strawman Has a Point: There's something to be said for N's claims — that Pokemon battles are cruel, selfish, and only result in Pokemon being hurt — on a normal playthrough. On a Nuzlocke run, he's pretty much right.
The Woobie: Chances are you will come across a character who has suffered so many hardships, be it the loss of a friend, a crushing defeat, or even personal matters, that you can't help but want to hold them and comfort them.
Fridge Brilliance: Giovanni is startled when Candace disguised as a Rocket greets him with "Hail Giovanni!", because he's not the leader of Team Rocket any more. She blew her cover.
Moral Event Horizon: Candace breaking and entering into the Olivine Town lighthouse, now a shrine to honor Jasmine who sacrificed herself to allow the rest of the town to survive, by way of Forretress' Mirror Shot to get the badge, considered a sacred object by the survivors, was viewed as this by some people.
Ship-to-Ship Combat: So much in her Pearl run, between Lily/Gary and Lily/Lucas, that she had to threaten to holler at the mods in the opening post of her Sapphire run. Gary won, if you're interested.
Petty's Nuzlocke Runs:
Harsher in Hindsight / Hilarious in Hindsight: Near the ending parts of FireRed, it was shown Petty's rival suffered immense injuries trying to capture Mewtwo, even losing an arm. Fast forward to 2013 and the same thing happens to Green in Pokémon Origins, but replace amputated arm with a broken one.
Jerkass Woobie: Gary Oak, playing strongly on the angry unfavorite interpretation.
Kynim's Nuzlocke Runs:
Ensemble Darkhorse: Kynim wasn't really expecting all the love Mimi got from the instant she joined the team.
Jasper the Joltik, who helps out N in Chargestone Cave, was a smash hit despite him being a one-point character.
Leif, Cheren's Serperior, became the first mon that wasn't under the ownership of either protagonist to get their own gijinka artwork due to demand after one of the White Extra comics helping Zach out.
Nightmare Fuel: The vision Skyla's fiancee gets when she touches Nina, displays a Hydreigon wrapped around her. Nina looks absolutely broken, and the scene is drawn with a creepy Art Shift. What is worse is that anyone who has played Black and White knows who the dragonbelongs to and knows what it can do. It makes it rather horrifying to wonder how it will play out.
Moral Event Horizon: Lyrax's Gold run immediately establishes the rival as a Complete Monster when he steals both of the leftover starters, apparently just so he could tell Lyrax "Don't follow me or I'll kill one of them." He does.
In Azza's Run:
Moral Event Horizon: Charmeleon (and his trainer as well) make it clear they're well over the Complete Monster line when Raticate argues that the murder of innocent Pokemon was completely unnecessary, and demands to be released from the team. They do so, but then Charmeleon claims that since Raticate is now a wild Pokemon, he can do whatever he wants, and very brutally murders Raticate as well.
The Unnamed Protagonist from Pitch Black is a terrifying, evil, sadistic protagonist. From the beginning it's established that he's NOT a good character, (Considering we see his first activities IMPALING POKEMON ON HIS PICKET FENCE). From then on, any Pokemon he catches he forces to fight and brutally murder his friends and family and sees them nothing more as tools, even going as far as to KILL his own Pokemon. Basically, he's an even worse version of Paul. His Oshawott, Icarus, MAY be just as bad.