Ok, first thing: this story is awesome. Haven't read A Wrinkle in Time yet, but I'll soon remedy that. Even though I didn't fully understand everything, I still got it, and I definitely love the ending!

Second, you're absolutely right: naming stuff is GREAT. I love how the show uses the idea of naming something to underscore John's immediate sense of possession over Atlantis, like, this city is his and he'll be damned if Aiden or Rodney gets to name something! :-D Hope that made sense...