In addition to its various episodic themes, there are other ideas that persist through the whole series.
A lot of the characters have the primary parental issues with their mothers or motherhood:
Quinn's mother goes into denial about her being pregnant and doesn't do anything to defend her daughter while her dad kicks her out of the house, only showing up at the last minute to try and make things right.
Quinn doesn't tell Puck that he can still invoke his parental rights if he wants to keep Beth (or she doesn't know), having previously told him that he was the reason she was giving their daughter up for adoption.
Her initial thought was to give the baby up for adoption. She didn't even consider keeping it. Granted, she is in High School still.
She didn't even consider aborting it either. (Though that could be caused by her religious background.)
In season three, she continues to want Beth back in order for self-fulfillment.
Rachel's mother manipulated another teenager into getting Rachel to contact her, dumped her when meeting her daughter did not live up to her expectations, and then adopts Beth right out of the blue without having made any preparations or learning anything about how to take care of a baby.
Finn's mother has some issues with letting go of her grief for her husband.
Kurt's mother is dead.
Puck's mother guilt-tripped him about his Jewish heritage.
Sue's mother left her daughters to go and hunt nazi's. Although she is anti-nazism, she called her daughter Sue Sylvester, which leaves her with the initials S.S.
This troper is still unsure if Sue's mother is actually hunting nazi's, or if it's just a wacky excuse for abandoning Sue and her sister...
Which would still mean that she is not such a good mother.
(same troper) that was my point, that would actually make her an even worse mother...
And the fact that Sue didn't even invite her own mother to her sisters funeral, because she tought that she wouldn't care, made it even worse.
Both times a parent of Dave Karofsky is called to the school, it's always his father. There's even speculation his mother either left or died like Kurt's.
Jossed David, after his suicide attempt, tells Kurt that his mum thinks he needs to be cured
Santana's parents are implied to have practiced Hands-Off Parenting, leaving her in the care of her grandmother, who wasn't exactly the nicest person.
Glee is often seen as a send up of the similar-at-first-glance High School Musical, mainly in the way it addresses teen pregnancy, homophobia (or just homosexuals), drug abuse, and other daily realities which are unable to be shown in the kid-friendly Disney Channel version of high school. This was apparently unintentional, as the show creator Ryan Murphy has stated that he's never seen HSM, though he admires it as a cultural phenomenon, and that he did not have it in mind when creating the show.
There's some debate whether or not the show is parodying the After-School Special or not. The entire episode "Wheels", the celibacy club scene in "Showmance" (and subsequent revelation two episodes later that its president is pregnant), the "Imagine" number with the deaf choir in "Hairography," and the statement about body image during "Home" can be read as ironic comments or completely straight examples of the trope. The idea is played for laughs with the pamphlets in Emma's office which mock the notion that you can fix a serious problem with pamphlets by giving them titles like "So You Like Throwing Up" for bulimia.
Much of the show can be seen as a deconstruction of traditional musicals, but especially Episode 10 "Ballads" which seemed intent on showing how singing your feelings doesn't work so well in real life. Kurt's advice for Finn to sing while thinking of "his" unborn daughter causes his mother to find out that Quinn is pregnant. Also, Kurt tells Finn to tell Quinn's parents through song about her pregnancy, resulting in a painfully awkward rendition of "You're Having My Baby." Finally, when Will is trying to shake Rachel's crush on him, Emma gives him the idea of letting her know through song that he's not available to her, resulting in a rendition of a mash-up of "Young Girl" and "Don't Stand So Close to Me..." which is so animated and sexy that it only makes Rachel (and Emma) swoon even more.
However singing their feelings was shown to work many times; Puck wins over Mercedes, Jesse wins over Rachel, Sam wins over Quinn, even Will easily wins over Sue - all through song.
Yeah, and how long did those relationships last?
Interestingly Ballads was written by Brad. He didn't write any of the episodes listed above where it worked. Depending on the Writer perhaps?
Episode 14 comes across as a major deconstruction of Dating Do-Si-Do, pointing out that you can't get over your ex immediately or automatically be ready for a relationship when the person you're interested in is available. Finn and Rachel, and Will and Emma fail right out of the gate, and Puck and Quinn are already having problems.
"Laryngitis" and "Funk" played with and deconstructed the idea of Crack Pairing in-universe. The relationship has potential, but ultimately it won't work out because the characters are too different.
Shannon Beiste. Big, tough looking female football coach with a manly voice who breaks down easily (and is heartbreaking when she does) and finds it very hard to handle the mockery she gets for looking and sounding like she does. She can't help it, after all. The only reason she lives up to her name is because of how defensive and insecure she is after being treated like some sort of beast throughout her life because of how she appears. Now admit it, when you first saw her in the season 2 promos you thought she was going to be a tough wrestler type with a heart of steel, a rival whose feelings weren't going to be taken too seriously and maybe used for comedy.
Rachel and Finn can both be read as deconstructions of the stock teen-show heroine and hero. Rachel's ostentatious 'good girl' persona, assumption that she's entitled to be liked, admired and popular because she's talented, and assumption that her life and achievements are the centre of everyone attention (whether positive or negative) as well as her own make her a ramped-up version of a stock 'put-upon' heroine; however, the episodes constantly contradict her own assessment of herself by making it clear that she's really not very important to anyone but herself, that having a good singing voice does not in any way expose her to the same discrimination and difficulties experienced by others such as Artie, Quinn during her pregnancy and Kurt, and that she's just as horrible to everyone around her as the 'mean girls' are to her. Similarly, Finn looks like a standard Nice Guy jock/leader whose Book Dumb appearance hides a smart guy who just needs to have the confidence to follow his own path - romantically or otherwise - in order to make the world a better place. However, it's repeatedly shown that he's heavily invested in staying at the top of the social pyramid, is much more of a follower than a leader, and has no ability to change the culture of WMHS and no real wish to. His genuine lack of intelligence and bad decision-making are also shown to have serious, negative consequences for more people than just himself, and are not compensated for by his occasional flashes of emotional insight.
Holly looks like the Cool Teacher that appears a lot in the media- a "hip" teacher who her students relate to. However, as we see more of her in The Substitute, we see that she doesn't really have her life together and she lacks the ability to truly care for her students, as seen when she doesn't help Mercedes and doesn't even know what her punishment was.
Brittany can be seen as a Deconstruction of the Dumb Blonde stereotype, making her a source of tragedy rather than comedy. Her intelligence seems to be low enough to suggest that she would be unable to cope in the outside world by herself. The faculty, save for Will, look the other way because of her position as a Cheerio, meaning that she never gets any help and no alarm bells go off for an underlying health condition. Plus, in a school where the average students think that a head of broccoli is a toilet brush or that women have prostates, are Britt's non-sequiturs really going to stand out? However, we do seem to be seeing the beginnings of Reconstruction - Although Brittany's continued belief in Santa Claus throws up some challenges for the rest of the club, it does help the other gleeks to get together to do something selfless. Also, her refusal to leave Artie for Santana demonstrates that she sees things in a very black and white, almost childlike way. She does what she thinks is right (and possibly tries to make up for her mistakes because she's realising that cheating with Santana does count) without falling prey to the brattier, more selfish instincts that virtually everyone else in the shows displays in romantic relationships.
Kurt is a Deconstruction of the stereotypical Camp Gay—his flamboyance makes him the most frequent target of bullying, which clearly takes a toll on him, and eventually he's forced to transfer schools when the bullying from one person goes Up to Eleven—namely, when Karofsky's antics gain a Villainous Crush edge, to the point where Kurt is terrified at the sight of him. Also, while he and his father have one of the most heartwarming relationships on the show, for a while he was so terrified of losing his father's love that he did very questionable things to keep it. The lack of anything resembling kissing or sex scenes until "Original Songs" is explained by Kurt's genuine discomfort and lack of information regarding sex, which isn't hard to believe for someone who is/was the only openly-gay kid in his high schoolnote note that most American public high schools have 500-1000 students.
Correspondingly, he's also a Reconstruction of the Camp Gay: his flamboyant fashion sense is a way of asserting his individuality because he'd rather do that than try to hide all the ways in which he's different from the other boys, and any minor-to-moderate cross-dressing seems to spring from his genuine belief that "fashion has no gender". His haughty, catty demeanor is largely a front, as flinging insults is the only way he can retaliate against his bullies, and as he gains more friends and stops fearing for his safety he becomes much warmer and less bitchy. He gets on with the girls better than the boys (at first) because the girls aren't afraid to be seen with him, and when the boys warm up to him later he gets on just as well with them. And not only does he get a real, on-screen romance, but the show averts But Not Too Gayhard and the relationship is treated like every other one.
But Not Too Gay seems to be getting deconstructed as well, judging by "Prom Queen."
In "Prom Queen," Blaine reveals that he got beat up at his old school for taking another openly gay boy to a Sadie Hawkins dance. At prom, the camera explicitly focuses on how Kurt and Blaine aren't acting like a couple—avoiding slow dances, standing about a foot away from each other, and constantly watching the other students. The only time they show their usual level of intimacy is in the hallway, where Kurt goes after he's voted Prom Queen as a malicious joke. Karofsky the Prom King cannot dance with Kurt because he's so terrified of what the other students will think, and when Blaine asks Kurt to dance with him instead, everyone apart from the New Directionsare quietly glaring daggers at them.
And finally, the second season's finale deconstructs The Power of Friendship and The Power of Love, as well as Technician Versus Performer. Writing songs at literally the last minute, having absolutely nothing planned in favor of goofing off in NY, and not caring about practicing for the last three weeks (instead taking time to sort out their personal issues and band together like the normally do) does not help their chances at all on a truly competitive stage, and they place twelfth, just two spots shy of qualifying. Vocal Adrenaline, who has been drilling non-stop and is not afraid to have more complex dances and songs, once again proves superior. The judges obviously did not care for the Finchel kiss, because while passionate, it was unplanned and impulsive and had no technical place... but neither that nor the Rachel-Sunshine pep talk were the only factors. Personally, I'm surprised they didn't place lower.
Karofsky was one of the main Season 1 villains and targeted Kurt badly enough to make him transfer, but the revelation that he's incredibly deep in the closet sparked an infamous flood of response. In a subversion of the standard story, his father is shown to be quite reasonable; the reason Karofsky's so conflicted is due to his peers and how he thinks he should act. Even then it's implied that the kids are so intolerant because the adults don't bother to enforce no-bullying policies, at least not homophobic bullying. Dalton is referred to as "unnaturally perfect," but it only looks that way compared to McKinley—would it really be hard to find a school with Dalton's level of tolerance? Karofsky is rapidly becoming one of the most well-received characters on the show regarding the sensitivity his conflict is being shown.
Blaine's sheer obliviousness regarding Kurt's feelings for him takes a darker light in Prom Queen: Considering that he got beat up for taking another boy to a Sadie Hawkins dance at his old school and how Kurt had to transfer due to severe bullying, it's not a stretch to think that Blaine might have been intentionally ignoring both Kurt's feelings and his own due to fear of something similar happening outside of Dalton.