Christina being unable to deal with Burke being shot makes a lot more sense after we learn that her father died in a car accident right in front of her when she was nine. However, she manages to overcome this, and fares much better when Owen is shot.
I don't know what your metric for faring much better is, but her reaction to Owen getting shot could not have been worse. She basically went on a downward spiral of PTSD from that day and ended up quitting her job. Granted, Owen being shot right in front of her was only one part of the reason she had PTSD from that day, but it was a fairly large part.
Owen and Derek refer to Meredith and Cristina as 'the twisted sisters.' This isn't just because they're so close, they balance each other out. Every time there is a intense trauma (the shooting, the plane crash etc.), Cristina is fairly calm but falls apart afterwards, while Meredith tends to somewhat fall apart during the incident and be fine afterwards.
April gets pregnant pretty quickly after getting married. This is likely because of her strong christian faith: she doesn't use much contraception.
Why don't many of the characters name their kids after the people who have died? Jackson probably didn't want to name his soon-to-die son after his dead mentor, Mark, and Meredith's pregnancy paranoia meant she probably didn't want to name her son after someone dead, and Derek's sisters probably already named a child after Derek's dad. Also, considering how everyone had sexual relations with each other naming them after others probably make it awkward anyway
Amelia is seen to be on edge when April and Jackson's baby turns out to have an illness meaning he'll die a few minutes after birth. Why? In Private Practice she had a similarly painful storyline and is reliving the experience. As she tells Owen at the end: "My baby lived for 43 minutes"
Owen's description of his perfect woman: Passionate about her work, doesn't care to cook or get out of bed if it's not a work day, sleeps soundly and peacefully, has suffered and understands suffering to the point that she accepts who he is and how he feels and doesn't want to change it. All of these describe Cristina (which is probably why he intentionally left out "someone who wants kids"). They also perfectly describe Amelia Shepherd, his future love interest who does eventually want a family.
Jackson is constantly embarrassed by his mother. One possible reason: imagine being a young boy whose mother is a famous urologist (one of her main specialities is as a penis doctor).
Episode "If/Then" (the alternate universe episode) has a lot of them.
Charlie who had been previously shot says at one point "Shoot me!"
Bailey in braids: a call back to an earlier episode where she was shown as a meek intern known as Mandy wearing cornrow braids.
Why would Kepner and Mer be friends? Mer hates her... oh, wait, Mer hates her because Kepner had a crush on Mer's husband, Derek in the real world. In this alternate universe Mer and Derek never got together, so Mer never hated Kepner for having a crush on her husband.
The "I'm just a girl in a bar" dialogue between Meredith and Derek is the same conversation they had in their first meeting.
The music has been used in previous episodes. "You Wouldn't Like Me If You Met Me" by Tegan and Sara was used in S1 E2; "Fools in Love" by Inara George was used in S2 E3; "Into the Fire" by Thirteen Senses was used in S1 E1; "Portions for Foxes" by Rilo Kiley was used in S1 E1; "Ruby Blue" by Roisin Murphy was used in S2 E3.
Karev says "I always say never mess with the crazy chicks," which is ironic because he was involved with Rebecca who went crazy and had to be committed and right after, he says "she's probably gonna go full-on Izzie," referring to the only other serious relationship he ever had on the show.
Cristina and Meredith have the "We don't have to do the thing where..." dialogue previously used in a few episodes, originating in S1 E1.
Why would Karev date Meredith and act like a good guy despite his backstory ? Because he knows that Meredith is the chief's daughter and could get favor by taking her last name.
The revelation of Amelia having a massive brain tumor explains a lot of her rather erratic behavior over the course of the series. Indeed, when brought in to consult, a mentor openly tells Amelia that this tumor didn't just spring up but has been growing for ten years. It has been compromising her impulse control and decision making for some time. "You are not of sound mind now and you haven't been for years." Thus, so much of Amelia's actions and personality going back to Private Practice that seemed wild are explained as caused by the tumor.
When they first meet, Maggie Pierce can't remember Jo Wilson's name, despite never messing up anyone else's name because Jo Wilson isn't her real name.
"You have apple hair. I threw a pancake in the river! The River!" It seems funny at first. Until it's not.
When Amelia discovers that she's had a brain tumor growing for a decade, it's her mentor who brings up the key issue: That Amelia has been operating on people for ten years with her judgement compromised, meaning so many of her "daring surgeries" were things no sane person would consider.
Arizona's very first piece of characterization (besides being perky) is in her second episode, where she reveals how scared she is of planes, wouldn't you be terrified if your nightmares later drastically came true:
"I wish I could get organs delivered instead of having to go pick them up [...] I hate flying, I always feel so much closer to death on a plane than in the OR, don't you?"
Owen did not break off his engagement with Beth until after the decimating ambush on his unit; presumably he also first appeared on the show and kissed Cristina before that ambush. That makes him a three-time offender of Your Cheating Heart. Yikes.
Fridge Brilliance for Callie being revealed to be such a good singer and named after the Greek goddess literally called "girl with the beautiful voice" (Calliope). What makes it meta? This was no accident: the part of Callie was written for Sara Ramirez after she won her Tony award, getting named that is a bit of an in joke and makes a damn lot of sense.