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.
Adaptation Displacement: Panchito's horse, Seņor Martinez actually comes from old American newspaper strips written in the 40s which, while popular in some countries, were never reprinted in English until after the publication of The Three Caballeros Ride Again
Anvilicious: Some of the stories (especially War of the Wendigo) move into this territory.
Crosses the Line Twice: A cheapskate who will read a newspaper from a trash can rather than buying one despite having a net worth of $900 billion is surely funnier than a cheapskate with a net worth of a few million who simply treats others like crap for his own gain.
Designated Villain: Surprisingly common. Quite a few stories have Rockerduck actually being far more benevolent than Scrooge, or simply being completely moral. He still always loses in the end.
Epileptic Trees: How Ludwig von Drake is related to Donald is quite a mystery. He is apparently Donald's uncle, but this would make him either Scrooge's brother or Grandma's son, neither of which seems likely since he is Austrian. Don Rosa has offered the possible explanation that he is married to Scrooge's sister, Matilda. Some German comics have Daisy calling him "Uncle".
Another puzzling relative is Gideon McDuck, a Recurring Character in the Italian comics described as Scrooge's younger brother, which conflicts with Scrooge's past as established by Rosa. Most fans consider him a half-brother from a brief relationship of Fergus McDuck's after his wife's death, but a simpler explanation is provided by this Italian family tree◊ where he is simply a cousin ("younger brother" thus likely being a term of endearment).
Rockerduck seems to appear more frequently in Italian comics than Glomgold ever did in American ones.
The Beagle Boys' grandfather appears much more frequently in Italian stories, but that version of the character appears to be solely based on the "Grandpa Beagle" from "The Money Well" and not on Blackheart Beagle from "The Fantastic River Race." Some of the versions make him more kind.
Disney comics in general are known to still be hugely popular in Europe, while they have largely faded out of American culture. Duck comics are no exception, and in fact seem to enjoy even more popularity there than Mickey Mouse ever did. This may be related to these comics being quite similar in style to Franco-Belgian Comics.
Gladstone Gander in the comics is widely regarded as an insufferable JerkassSmug Snake who delights in rubbing his constant stream of good fortune in Donald's face and never suffers for it, and for whom Daisy is often more than willing to forsake Donald's affections.
Bubba the Cave Duck & Tootsie the Triceratops in DuckTales are viewed as unnecessary and unwelcome additions to the primary cast. Their ever-increasing time in the spotlight in later episodes didn't help.
Scrooge can also qualify for his jerkass tendencies, particularly for Donald's fans. You'll hear "When will Donald get his revenge on Gladstone and Scrooge?" from Donald's fans quite often. This is part of the reason behind the creation of Paperinik.
The Woobie: Ms. Emily Quackfast. One thing that does mostly remain consistent is her really low salary. Also Webby on DuckTales.
There is some variation to this; at times she is presented as so competent and invaluable to the McDuck industries that even Scrooge couldn't run things long without her, and as a result she gets a raise every time she brings up her oncoming vacation time.
Fenton on DuckTales. While mostly played for laughs, sometimes the guy really needs a break.
Donald himself skirts the line of woobiehood, especially any time he appears with Gladstone or Scrooge (or even, on occasion, his nephews). It's only partially offset by his own stubbornness and short temper.
Though it's obviously never brought up on panel, there is legitimate horror in Huey, Dewey, and Louie's backstories. They were abandoned by their mother on Donald's doorstep, to be raised by their generally well-meaning but somewhat questionable uncle. And if you throw DuckTales in as canon, Donald himself abandons them. Glimpses of the future suggest he never returns, and he's not mentioned again after the second season premiere. At the very least, one imagines a great deal of therapy in their future.
Don Rosa's "The Life and Times of Scrooge McDuck" series flirts with this portrayal for Scrooge. By the penultimate chapter, it's hard not to feel bad for a man who let his obsession with wealth chase away his family and friends and turn him into a bitter old Citizen Kane expy. Of course, he's very much the author of his own woe, and the story concludes with his reconnecting with Donald and the nephews, so it doesn't stick, but it's a rather depressing insight into Scrooge's character.