Leliana's "death" is explained in DA2's Sebastian DLC She tells Hawke and his/her party that "The Maker decided it wasn't my time yet." if she died. I kept her alive.
The main choices I saw that have any affect would be any chance you got to side with the Templars or Mages or the ones involving your party.
Carver/Bethany's fate: Grey Warden, dead, or Templar/Circle Mage
Sebastian/Ander's fate: Sebastian leaves if Anders lives, but if Hawke kills Anders, Sebastian stays. While Anders is a mandatory party member, Sebastian isn't.
Merrill's fate and her clan's: If you choose the Friend Route, Hawke and his/her party will slaughter Merrill's clan, but if you follow the Rivalry path, Merrill will be an outcast to her clan. You can choose whichever path you want, but those are the points you'll gain if you want to be Merrill's friend or rival. If you side with the Templars, Merrill can be persuaded by Anders to not follow Hawke and should Hawke not convince her otherwise if her Companion quest hasn't been finished, she will be killed by Hawke. Merrill is a mandatory party member
Isabela: She either kills the man she's been avoiding, takes his ship, runs away, taken by the Qunari, or Hawke can never meet her.
Fenris: You can either refuse his services (he's not a mandatory party member), turn him in to his master, abandon him when he goes after the woman who tortured him, or kill him if you side with the mages and his personal quests haven't been completed.
Varric: Varric stays with you no matter what. His brother betrays him in the Deep Roads and during his personal quest you can either kill his brother, let him live, or have Anders heal him to clear his head; you'll then be given the same two options before hand although letting him live now gives Varric friend points and killing him gives him rivalry points.
Aveline: You can have her marry a guardsman to allow her happiness or not. If Hawke sides with the mages and her personal quests haven't been finished, she refuses to follow Hawke anymore. She'll never die, but she is a mandatory party member.
Now, there are 7 Mage vs. Templar choices:
Act 1
Have Feynriell go to the Dalish Elves (Mage) or the Circle (Templar) to practice his Dream Walker magic
Turn over mages that fled Templars (Templar) or help them escape by either lying to the Templars outside or killing the Templars (Mage).
When telling Cullen about Templar recruits being possessed, have the Templar Keran be stripped of his Templar status (Mage) or allow him to stay as a Templar (Templar)
Act 2
When encountering Feynriell in the Fade, either allow him or convince him to train his magic (Mage) or make him Tranquil (Templar)
Near the end of Act 2, agree with Orsino (Mage) or Meredith (Templar)
Act 3
Make Emile de Launcet either return to the Circle (Templar) or let him go free (Mage)
Either argue in support of the mages (Mage) or for the Templars (Templar)
I believe all of those are the major choices