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.
Anvilicious in its free-market capitalist propaganda. Warbucks "died" when FDR was re-elected because the New Deal was so bad for self-made men, but reappeared after FDR died as the USA was now worth living in again.
The scene in the movie where a stereotyped Bolshevik tries to kill "Daddy" with a bomb because Mr Warbucks is "living proof that the American System works and the Bolsheviks don't want anyone to know about that." is subtle by comparison!
And, of course, had Gray been alive when the musical debuted, you know he would have been completely livid for the scenes with Warbucks praising FDR.
Arc Fatigue: Gray would let storylines go on for quite a while in order to make the resolution more satisfying. This usually didn't result in this trope, since he'd include some subplot for the readers to follow or at least have the story develop, though it did so slowly, but the arc from 1933 in which Annie and her new friend, blind violin-player "Uncle" Dan, make a living as professional musicians and get cheated of their profits by their manager Chizzler spends a couple of months with every strip just pointing out that they're getting cheated, showing them performing, or having Chizzler laugh in private at Annie and Dan. This is one arc that definitely could have been shortened without any loss in quality.
Archive Panic: IDW have been publishing collections for a couple of years. So far, eight collections have been published, each of them very long.
Canon Sue: Subverted with "Daddy" Warbucks. At first he's the guy who can solve any problem. Do the Silos need money? Don't worry, "Daddy" is here! Somebody captured Annie? Don't worry, "Daddy" is here to beat that someone up! (If there are more than five "someones," "Daddy" might have to call for back-up.) However, later it turns out that he's got his weaknesses as well. Trixie Tinkle tries to trick him and he falls for it. The Shark makes an attempt at bankrupting him and he doesn't have the financial skills to stop it. When he's living in a cheap apartment with Annie he can't manage to land a job for a long while. It becomes increasingly clear that he's got his limitations, just like anybody. The reason he seemed perfect in the early stories is that all the problems was of the kind that can be solved by beating somebody up or paying enough money.
Fair for Its Day: Wun Wey, the clever Chinese man who is a friend of Warbucks, wouldn't be acceptable in our time with his secret scheming and planning, but in the thirties he was a very progressive and unusually non-racist portrayal of a Chinese-American individual, mainly because he was a Chinese good guy who wasn't an Ethnic Scrappy. It's noticeable that the Chinese people in the strip aren't universally good or bad; it varies from person to person. There's Wun Wey and his friends, they're good people who help Annie out. There's the Tong men who at one point are after Annie, horrible criminals. Like all other people, the Chinese in the strip are individuals, some of them good, some of them bad. In other words, Gray actually suggested that a person's value wasn't determined by their race.
Family-Unfriendly Aesop: one World War II strip has Annie seeing a man physically attack an obnoxious war-profiteer for declaring that he hopes the war will continue for another twenty years. When a policeman tries to intervene, Annie stops him because "it's better some times to let folks settle some questions by what you might call democratic processes."
Franchise Original Sin: At some point, early on, the Maybe Magic, Maybe Mundane scenarios, such as Punjab's mystical abilities, became open displays of magic. After that, introducing ancient beings, demons and even God himself was a regular feature of the strip.
Informed Wrongness: Mrs. Warbucks donate large amounts of money to charity. However, she doesn't care a bit about the poor, she just wants to be praised and give a good impression. Fact remains that the poor probably wish more people were like her. Motivation aside, she does help the needy, and that's a good thing.
Iron Woobie: Annie goes through a lot of trouble, but she's tough enough to take it.
Tear Jerker: A robber has kept Annie with him so that the police can't shoot at him because of the risk of hitting her. He finally decides to send her away.
The robber: I'm not going to take any more chances o' letting you get hurt. I'm not that bad. I'm still man enough to meet my finish alone.
Pertty much the first 2/3rds of the year 1934.
Uncanny Valley: Everyone's eyes are completely white. In a 1931 interview, this explanation was offered:
Gray: They ask me why I don't put pupils in the eyes of my subjects. In the first place, I don't think it is necessary, and again, even if I did put them in they wouldn't show up when reproduced in the majority of newspapers.