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.
Designated Protagonist Syndrome: Arnold definitely gets some flak for his characterization post-Flanderization, where he becomes something of a messiah to contrast his quirky classmates.
Ensemble Darkhorse: Curly is easily one of the most popular characters with the fandom.
Helga also grew in popularity due to her compelling Character Development, by the end of the series, most people would think she was the main character instead of the football head due to how much spotlight she had. In fact, the show was meant to have a sequel specifically geared around Helga as the main focus in high school.
"Funny Aneurysm" Moment: At the end of "The Flood", as floodwaters surround PS 118, Principal Wartz stands on the roof of the school singing, "Way down yonder, in New Orleans..."
Harsher in Hindsight: It was once implied that Helga's dysfunctional home life was the end result of her sister Olga moving out (as her parents favored Olga over Helga), leading her dad to push Helga to be more like her older sister while Miriam became a covert alcoholic (or "smoothie" drinker) just to cope with dealing with a Jerk Ass like Bob and a bratty daughter like Helga. The episode "Helga on the Couch" revealed that Helga's been neglected by her parents since she was preschool-aged and that her secret crush on Arnold was the first time anyone has given her any sort of affection in her life.
Well, actually, she does/did have a fanbase for her appearances in Seasons 2 and 3 (hell, she was actually The Woobie when she first debuted!) It was mainly due to the Romantic Plot Tumor love triangle of Seasons 4 and 5 (and accomponying Die for Our Ship sentiments) that pushed her into Scrappydom.
An even bigger Scrappy than Lila who yet only appeared once is Iggy from the episode "Arnold Betrays Iggy". It doesn't help that the episode itself ends on the note that Iggy has gone beyond Arnold's forgiveness.
Gerald's little sister Timburly gets a lot of hate in fandom mainly for being really annoying and is usually hindering Arnold and Gerald's plans in any episode where she plays a key role. The best example of this is the "Chocolate Turtles" episode.
Seasonal Rot: Seasons 4 and 5, mainly due to Arnold's character becoming bland and the Arnold/Helga/Lila love triangle becoming a Romantic Plot Tumor (contrast to Season 3, where it only came up twice and actually seemed to be resolved within those two episodes!) There were still some good episodes here and there, though, particularly "Parent's Day" in Season 4 and "The Journal" in Season 5.