One of the plotlines in the third season is whether Lindsay was adopted, which would mean that George Michael and Maeby were not biological cousins, and free to pursue a romantic relationship. In the very first episode, the narrator referred to "George Michael's cousin, Maeby" ("George Michael's cousin, maybe.")
How the hell did George Senior manage to get upgraded to house arrest after his numerous escapes/escape attempts? What judge in their right mind would let him out of jail? But rememberd the setting for the show: Southern California. The same place that sentenced Lindsay Lohan, Khloe Kardashian, Paris Hilton, etc. Special treatment capital of the world. While still infuriating, it IS Truth in Television.
GOB is of course, short for George Oscar Bluth, a bizarre combination of nickname and monogram. Where could they have come up with this? Possibly from John Ellis Bush, better known to us as Jeb (once you see the parallels between the Bluths and the Bushes, you cannot unsee them).
None of the Bluth children use their real name: Michael is actually Nichael due to a typo on the birth certificate, Lindsay's real name is Nellie, George always goes by GOB, Byron is always called Buster and Annyong's real name is Hel-loh.
On a similar note regarding the names of George and Lucille's children, notice how most of the Bluth family seems to have the names George, Michael and Oscar or some variation of those names. The only kids to not have these names are Lindsay, Buster and Annyong which makes sense seeing as they're not really George and Lucille's kids - Lindsay and Annyong were both adopted and Buster is Oscar's son, not George's.
So who is Buster's father? Although the last episode of Season 2 essentially reveals that it's Oscar, Buster will never know for sure because as twins, George and Oscar share the same DNA.
The episode where Justine Bateman cameos, Michael is surprised and disturbed by her trying to seduce him (since she's a prostitute), thinking that they're related. Well of course, they are.
There are oh, oh so many hints dropped throughout the show that Lucille was really the one responsible for all the awful things the company did, the most blatant being her telling the press that George is "hardly a criminal mastermind" in the pilot episode. But the one that makes it the most obvious is that George, for all his schemes, manipulations and so forth, is the only one of the two consistently shown to actually care about his kids—from his distress at Michael and GOB falling off the balcony to his constant thanking of Michael for looking out for him to paying off his inmates so they won't sexually harass Lindsey when she visits him. (His complete disregard for Buster can be explained by the fact that Buster's not his son, and his resentment of Oscar over the affair could easily have trickled onto Buster, especially given that he was left to raise him after having already gotten three kids.) Any moment Lucille appears to have of genuine emotion, on the other hand, always turns out to be just another way of manipulating them. In fact, George Sr. taking the hit is easily explained by the fact that he seems to genuinely care for Lucille even if Lucille doesn't seem to reciprocate.
In "The Sword of Destiny", an old man in a Chinese tea shop sold a "priceless" artifact to GOB at the drop of a hat. Why would he do that? He sold him a katana (a Japanese sword) and anybody who knows their swords will know that he was obviously messing with him.
In "Good Grief", Lindsey reveals that she used to use the thought of George Sr's death to get her going when she pretended to cry. So, why did she fail to pretend to cry in the pilot? Because her father just got arrested for multiple crimes which have caused her to lose her family income. So now, she's probably lost most if not all respect for her father and now wouldn't mind him dying.
In the Pilot, Michael asks George Michael what they always say the most important thing is. George Michael answers "Breakfast" before Michael corrects him with "Family". In "Development Arrested", Michael repeats the question. This time, George Michael answers "Family" before Michael corrects him with "Breakfast". At first, it looks like a simple Call Back. On closer examination, it's an indication of how much the events of the series have dampened his appreciation for his family.
Many have noticed how the worst sides of Michael's personality have been exaggerated in season 4, but there might be a good reason for that. Just when he had finally decided to break completely off from the family for good and start his own company, the housing bubble comes along and hits him at the worst possible time. Michael have essentially realized that, even when he is free of his family, the world is still filled with people who behave like the Bluths and they just managed to screw over him again. Who wouldn't go a little insane after having something like that happening to them?
The alternate interpretation is that Michael was always a terrible person and only seemed decent relative to the other Bluths. When we mostly see him interacting with ordinary people, he comes across as terrible... because he is. (His treatment of George Michael throughout the series is the strongest evidence of this theory.)
In the Season 4 episode "Double Crossers", GOB and Michael discover several cases of Mike's Hard Lemonade in a house that was supposed to be abandoned. Michael first suspects Lindsay of stashing the product there, then changes his mind to believing that Tobias did it (The Narrator reveals it's neither). After thinking about it, Michael was right in suspecting Tobias: Who else would buy several cases of a product simply because it says "Mike's Hard" on the packaging?
The joke about Attitude, the gay magazine from the UK, seems like a one-off joke at first, until GOB's second episode titled "A New Attitude", in which GOB pretends to be gay in order to get revenge on Tony Wonder.
Michael hooked up with Rebel because she reminded him of his late wife. George Michael is also dating Rebel due to some wacky mishaps. Ergo, George Michael is dating his mother. Man, George Michael just can't get away from this whole incest-but-not-really situation can he?
"A trick is something a whore does for money, or c—", Gob starts in one episode, before the bartender tells him an illusion won't cover his tab. Was he going to say "cocaine", as in the extended pilot, or "candy", in the aired version? It doesn't matter—the real reference is to the fact that the line got changed in the first place.
A big theme in season 4 is that the characters are too selfish to change for the better, and that even when they overcome a quirk from the first three seasons, they replace it with another, similar one. With that in mind, Michael's relationship with Rebel seems to parallel his relationship with Rita earlier in the show. Both women are played by an actress doing a Fake Nationality (Charlize Theron, who plays Rita is a naturalized American from South Africa who usually acts in an American accent, and is a Fake Brit here; Isla Fisher, who is Australian, is a Fake American here), and Michael has an inaccurate understanding of each woman's relationship with a male associate (Michael thinks that Rita's uncle/caregiver is The Handler; Michael thinks that Ron Howard, Rebel's father, is her controlling boyfriend/sugardaddy).
Gob's insane ramblings during season 4 are foreshadowing of his sexuality and/or his being trapped in a roofie circle, but one particular line in episode 5 is noteworthy. When speaking to Tobias, who says that Gob 'looks like he (Tobias) feels'. Gob replies, "Gay?", which seems like another Transparent Closet joke about Tobias. After the whole season wraps up, it becomes apparent that Gob was desperately seeking someone who might understand what he was going through - Tobias was too conditioned to laugh such statements off to notice it.
Notice how Marvel is so trigger happy with cease and desist orders? Season 4 took place around before 2013. Marvel was bought by Disney, who by the way has the lawsuit happy reputation, in 2009. This can also explain why Marvel lawyers were at Disneyland.
In "Altar Egos", Maeby hires George Michael to mark the correct answers onto a test she took. She even got her name wrong, which she puts as S. Funke. She provides a ridiculous explanation about the school wanting students to put an S. if they're single and an M. if they're married. However, later in the same episode we find out that she's invented a fictional sister Surely as part of a scam, and has been taking tests as Surely (S. Funke), and then re-taking them with the correct answers as Maeby.
DeBrie was in a Fantastic Four movie that ended up being so bad, it got featured on Mystery Science Theater 3000. But it gets worse when you look at the details: the movie was made in 1992 and the episode featured Joel. Since Joel left the show in 1993, that means the movie managed to get on MST3K in less than a year. (Then again, licensing the film out to the show could've been the only way to recoup the costs.) The production is based on Roger Corman's infamous adaptation, filmed in less than a month and intended for release in 1994. This means the version shown in Arrested Development is not only so bad they could only get the MST3K version, it was even more of a disaster than the real life one.
In Season 4, fans found the inclusions of flashbacks featuring Kristen Wiig and Seth Rogen as Lucille and George Sr. a mixed bag. However, when you realize that the "flashbacks" are actually dramatizations and Wiig and Rogen are literally playing them in the documentary, it totally works.
In-universe: The destruction Buster caused when the army exploited his man-child innocence by assignment Buster to what he thinks is a video game. Buster does not react well upon the revelation.
Due to the real life execution of Saddam Hussein, it's hard not to think about the fact that in the Arrested Development universe the one who got executed was a lookalike who was forced to take his fall as revealed near the end of season three. The worst part is, the real one is at large.