Charlie keeps referring to Manny Quinn as gay because of the alleged quoted Rose gives him. After he and Rose have sex, he runs out, and Manny falls out... of the closet.
Notice the title given to the show was Two and a Half Men, as Jake was still a kid, so he was the half. Now that Jake is grown up hes already a man, but Walden Schmidt is mentally a kid. He even takes Jakes part in the opening sequence.
When Alan first meets Walden, he laments that he is "hung like a freakin' elephant". Walden just came from the ocean, which he remarked was freezing cold. Now, we all know what cold water can do to a person's manhood... it may in fact be even bigger.
Charlie's being a even bigger asshole in Season 8 makes sense, he's probably secretly dealing with losing Chelsea and it's how he dealt with it to feel better about himself.
Judith's declining role in the later seasons makes sense given that the only reason Alan put up with her shit was to retain custody of Jake. Once Jake graduated high school and went off on his own, Alan no longer needed to be bothered with her in his life.
Charlie Harper was once stated by a character to have slept with the entirety of the Sacramento area's female population, and was implied to have (however unknowingly) slept with people who were possibly married. The amount of people he slept with (in one episode its even implied to be on sight), which would have enough to have him either head for a venial clinic or have mandatory sex-offender registration and yet is even allowed to do some of these things in the public is... genuinely horrifying when really thinking about it.
It's more likely that Charlie's friend was exaggerating, and he expressed disgust at the idea that Alan thinks he slept with the two 16 year old girls who Jake may have slept with at the start of Season 8.
Jake's becoming even stupider then ever may be a result of both Judith and Alan giving up on him and not encouraging and motivating him and raising him.
The series finale reveals Charlie was never killed. So..... whose remains were in the casket that was actually buried?
The episode says it was actually a goat's.
And the ghost that visited Alan in the hospital was really a hallucination.
Despite this, Charlie is revealed to alive and real. While it's heartwarming that he gave money to the people he liked the most, it's implied he was going to murder Alan and Walden (the people he hated most) in the finale.
Alan Harper was RAPED by Melissa's mother. She gave him that "special" banana bread, and then the next thing he knows, he's having sex with her. Due to being seriously doped out of his gourd, there is no way he could have consented. And somehow he's the one kicked out instead of Melissa's mother.