Some choices in the original game are gone from this, such as choosing whether or not to get new armor after enchanting your weapon.
In the original game, Soren wears armor throughout the entire game. In the games files, there is an unarmored version of him that isn't seen in the actual game. The Minecraft Console and Bedrock editions have a skin pack based on the game, which includes both versions. The Netflix series uses Unarmored Soren for unknown reasons.
The original game gives you six options for Jesse's Appearance, three male and three female. This game only has two options, one male and one female.
The beginning of Episode 1 includes an exclusive intro with Petra telling you how to play. She also introduces you to the Male and Female Jesse's, so you can pick which one you want to play as.