1) Tris and Four: The movie did well with building up their relationship, but there was still a couple things missing. Let's start with the fact that both these characters come from a faction that doesn't really boast emotions. Actions like PDA and teasing isn't something Abnegation does. So there is a lot of insecurity in their relationship: Tris' insecurity about why Four would choose her as a companion. Four's insecurity of removing his shirt in front of Tris. Both their insecurities in being intimate with each other. I thought this aspect in the book brought an interesting vibe to their relationship. Both are new to it and grow and experience it together. That wasn't in the movie.
What also wasn't in the movie: Four saying I love you on the train ride to Amity. In the movie, Tris says it first as Four holds the gun to her forehead. This to me wasn't true to her character. One of Tris' fear is intimacy. Saying something like I love you takes time even if she does feel it. In fact, it becomes an elephant in the room in the second book. It takes her more than half the second book to say it and even then, Four was asleep.
2) Edward: The scene where Peter stabs Edward in the eye was deleted from the final version of the movie. But what also disappears, was Edward himself. It was like one minute he was there in the number one spot and the next he was gone with no explanations. This wouldn't have been a big deal if it wasn't for that fact that Edward plays a bigger role in the second book with the factionless. I assume the movie makers will just transfer that over to a different character. Guess I need to watch the movie to see.
3) Christina and Tris: Most of their friendship was portrayed well in the movie. All but one: Capture the Flag. This is the first time that Tris shines in Dauntless and Christina is jealous. So jealous, that when they reach the opponents flag, Christina patronizes Tris into letting her physically capture it. "You're already the hero of the day," she says. This is when Tris realizes that any of them will do whatever it takes to make it into Dauntless, even her friends.
As I said, as a movie, it was good. But as an adaptation, it needs a bit of tweaking.