Anyhow, just a few thoughts I have: keep in mind that I first read A Wrinkle in Time when I was eight, and that it's largely responsible for my love of science-fantasy and time and space traveling heroes, and the series as a whole may have had an unacceptably broad influence on my worldview.
2) It's extremely hard for me to identify with Meg as an adult. Once Meg is no longer needed in the story to be Charles Wallace's devoted guardian, keeping him safe until such time as he can save the world, she essentially disappears within the interconnected L'Engle world. This isn't just because she's no longer a main character, or because the books are generally YA and don't swing back to her family until her eldest daughter hits her teen years: Meg's powers of empathy and telepathic communication (Kything, in this continuity,) are second to no one besides Charles Wallace, but after A Swiftly Tilting Planet, Meg's identity is pretty much erased. Her only narrative purpose now is to support her husband (and to provide him with her family connections, which advance his research considerably,) and to raise the next heroine, her oldest daughter Polly. I suppose you could say that she becomes a spiritual anchor for her family, but the truth is that by An Acceptable Time, the last novel clearly set in the Time universe and the only novel after the Time Quartet to return to the Murray family habit of time and space traveling, all of Meg's character development in A Wrinkle in Time, and A Wind in the Door, has been completely undone, and she's developed an inferiority complex about her intelligence, and chosen to be a stay-at-home mother primarily because she "doesn't want to compete," with her mother, a Nobel Laureate. This is despite the fact that she has an unfinished PhD in math and her mother is a cellular biologist. Meanwhile her other brothers Sandy and Dennys, the "Merely" slightly gifted family members, have no problems becoming a lawyer and a surgeon, respectively.
The thing is, during the first two books of the Time Quartet, Meg receives comparable training to Charles Wallace, is offered equal or greater opportunities to travel through time and space, and formed the basis of her romance with her future husband Calvin by dragging him along to learn the secret spiritual mysteries of time and space along with her. Yet Meg's importance to the universe is thrown by the wayside as soon as she has a child, despite the fact that she's canonically of equal or greater intelligence to her father and shown to be capable of both kything (telepathic communication between souls) and tessering (teleportation via... string theory, sort of, which normal humans are not equipped to handle.)
Does Meg have the right to chose to become a housewife and spend most of the ten years after A Swiftly Tilting Planet homeschooling her seven children? Yes. Do I understand her choice? Not at all.
3) Whatever happened to Charles Wallace? All of the L'Engle books featuring the Murray/O'Keefes, the Austins, or their reaccurring family friends like Canon Talis or Zachary Gray are set in the same, continuous crossover universe. Time has been substantially altered only once, at the end of A Swiftly Tilting Planet, and altering time into it's current shape was the world-altering task that Charles Wallace, supergenius child savior, was born to do. He's mentioned once or twice in later books featuring Meg's daughter Polly, as Polly's favorite uncle who is almost never there. While it's implied (especially in Arm of the Starfish, where Polly is just a hair too young to be the only main character,) that he keeps in touch with Meg (and possibly their mother, from whom they inherited the ability to kythe in the first place, though hers is rudimentary and untrained,) over their long-established telepathic connection, and that he might not even spend much time at all on earth or in this time, since he's been trained in tessering and kything by the L'Engle universe's versions of angels, and it was mentioned several times that Earth wasn't the only planet he would save. Presumably, he's out fighting the Echeroi (a cosmic force of hate and destruction, made up of souls that achieved non-being through hating... it's complicated, okay?) one star or soul at a time, but since Meg is no longer the main character, I can only presume that. Maybe she's living a double life, with half her soul and consciousness helping out Charles Wallace, and that's why she's satisfied with her life on earth as a wife and mother.
4) I dislike Vicky Austin as a protagonist. She's too passive: the Austin books are not about Vicky, they happen near Vicky. She later writes poems about them. Her identity as a poet and the "soul" of the family is especially grating compared to Meg's more proactive role as the soul and the spiritual protector of the Murray family, and she doesn't come into her own as a narrator or a character until near the end of A Ring of Endless Light, the fourth book that she can really be considered a character in. Her social and intellectual identity as a teenager after The Young Unicorns revolves around her love interests, and her eventual ability to Kythe (also in A Ring of Endless Light,) with her love interest Adam is somewhat cheapened by the fact that it exists mostly to rescue her from a mental breakdown. The fact that Vicky is used during A Ring of Endless Light and The Moon by Night to build the basis of Zachary Gray's redemption by being his love interest is also annoying, especially since the job is "finished" by Polly O'Keefe, who is two years younger than her and most definitely a minor when she replaces Vicky as Zach's love interest. (Actually, I think Zach is older than Vicky too, but I don't think there was ever an underage problem there - he's in college when he's pursuing a relationship with Polly during the second to last book, A House Like a Lotus.)
5) Why are all the heroines defined by their support or spiritual rescue of their male family members and love interests?
Maybe it's L'Engle's background: she was born in 1918, which could explain why most of her major romances contain men in their early twenties pursuing relationships with sixteen and seventeen year old girls. (except for Meg and Calvin, who attend both high school and college together. Calvin is at most a year or two older than Meg.) Maybe it's the only way she could get science fantasy with female protagonists published in 1962. Maybe she wanted her protagonists - Meg and Vicky are both based on her childhood - to have the same accomplishments she did, namely a husband and children.
6) I'm ambivalent about the "othering" of high intelligence in the Kairos (Murray/O'Keefe) half of the continuum. While it's clear that Madeline L'Engle believed that high intelligence and high empathy were good things, and that she wrote ultimately sympathetic characters of more typical IQ, the fact remains that by writing Charles Wallace as a metahuman and the rest of the family as approaching the metahuman, she reduced the ability of the reader to identify with them, or to see them as ordinary human beings instead of mystical spiritual saviors.
7) Why am I still writing about this? I desperately don't want to do any more Spanish homework.