This episode wasn't actually all the "What if?" questions that Meredith asked in the opening monologue. For those that have been watching for long enough, and bothered to pay enough attention to remember some of the more interesting details, the scenario we saw was the scenario that Richard gave Ellis when Ellis was near death. He told her that he should have chosen her, and that Meredith would have had a caring father and a stable home, and Ellis would have been healthy and happy.
Here's the problem with that "What if?" Ellis Grey, the surgeon, is a terrible, competitive person that beats down anybody and everybody. Ellis Grey, the mother, is just as neglectful and controlling as she ever was. This means that almost all of the changes are for the worse. I'll do this by character instead of timeline, and it'll only be what happened BEFORE the episode. Everybody else has already done reviews of the episode. I'm only going with characters we saw in the first episode of the series AND in this episode, though I'll also explain the write-offs (and in one case, on).
- Chief Weber: With Ellis being chief instead of Richard, Richard isn't the respected elder surgeon that everybody knows and reveres. He's just another attending, who happens to be married to the Chief of Surgery. It means he has less authority than he normally would, and apparently has less confidence than he usually displays. However, he is a GREAT father, to the point where he adopted Meredith and she took his last name.
- Meredith: Meredith is a shiny, happy person because she grew up with a loving father. She went to Mercy West for her residency instead of Seattle Grace, and became friends with April. She came to Seattle Grace after that hospital absorbed Mercy West, and presumably moved back in with her parents to be close to the hospital. Reid (you know, the first victim in the mass murder at the end of S6) took her place at Seattle Grace. She never knew Izzy, George, or Burke. She has also never met Lexi.
- Derek: Since he didn't meet Meredith after coming to Seattle, he got back with Addison (okay, so I'm covering both of them). He's still miserable in his marriage, and with Ellis as his superior instead of Richard, he feels like nothing he can do will get noticed, and knows that Ellis prefers Addison, and Addison has a baby. Thus, he hasn't taught, and hasn't done any research, even that brain surgery method she developed with Meredith.
- Bailey: Without Richard as the Chief pushing her to speak up and be better, she stayed the quiet and shy woman she was in that "Time Warp" episode. This meant that she never learned to advocate for her patients, even when she really needed to. She also isn't all that good when it comes to residents and interns. She motivates absolutely nobody, and just sticks back and lets Ellis Grey be Ellis Grey.
- Cristina: Burke left because he slept with her, as Ellis Grey would have fired Burke, unlike Richard, who appreciated that Preston came forward, and that they were both unattached to anybody else. Since Burke left because of her, Ellis wouldn't give a damn what she thought of any other cardio attending, talented or not. Without Meredith as a friend, she never bonded with anybody else - well, maybe Reid, but Reid is still dead.
- Alex: Karev never moved in with anybody else, and stayed a jackass. Without Meredith there, he blew his one shot with Izzy, meaning he never got close to her. His arrhythmia was misdiagnosed as vision problems, hence the glasses. He's still messed up because of family issues, but without an Alzheimer's trial, or a reason for Meredith to interfere in it, Karev's natural leadership skills came through, and he never betrayed anybody. One thing stayed the same, though - being around Meredith made him want to be better, and he screwed it up.
- And Honorable Mentions: Ellis fired Preston Burke when he admitted to having a relationship with Yang. The reason O'Malley disappeared after failing his Intern exam was that Bailey wasn't a strong figure, and therefore didn't have the authority to encourage him to re-do his Intern year. Reid is still dead, but most likely because she ratted out Stevens, and therefore was killed when Izzy came back and shot up the hospital. Ellis isn't the type to care about plastics, so Sloane was never hired to the hospital. The rest is explained in the episode.
In summary, Meredith may have wanted Richard to admit he should have chosen Ellis in the past, but truthfully, she would have been more miserable. Oh, and Yang and Meredith are destined to be friends, while MerDer was always destined to happen after Derek discovered Addison cheating on him.