Can we get choices that really matter and have a effect?

[DPZ2]

Not saying anything major like good/evil choices but sometimes through the story I personally would have made a choice to Join with zenos or help Emat

Choices have consequences.

In the case of one of your favorites, Emet, you don't learn enough about what you appear to consider The Truth until it is too late. Your choices at that point are

(a) die in an explosion of light that triggers the next calamity or (b) fight and defeat Emet.

Option (a) is End of Story. You aren't invited to the after-party. You can now unsub as you've won(?) the game.

Option (b) plays out as it does in game.