Players should not be punished for not magically knowing what class they were supposed to have picked at beginning the game for the outcome they prefer. Nor should they be compelled to play a class they don't actually enjoy or enjoy less than their preferred class to get the version of the story they want. It's horrible writing and horrible game design.
It's not punishing players for not knowing what class benefits which quests specifically.
It encourages replayability and help gamers figure out the kind of protagonist they want to be, with the class having extra content outside of the combat.
What 'options' are these? What are the consequences? Are all rewards and all outcomes ultimately available to every class? How does this involve the other squadmates? Are some options clearly more fun than the other?
More content.
If a soldier gives excellent tactical advice to the garrison before a battle, or an engineer is able to power up some turrets and repair some mechs, or an adept is able to set up barriers to protect key points, the overall outcome is the same. Less casualties done with the class's own unique flair.
As for what's more fun than others, that depends on the gamer. I'm having a huge blast right now in ME1 as an Engineer, finding the combat to be incredibly easy, easier than the time I had as a soldier despite playing on a higher difficulty, and I'm enjoying it more than I did playing a soldier, and I enjoyed Adept just as much.
It's really nothing more than preferances of the gamer. Say hypothetically you enjoy playing as a soldier, you'll probably have more fun with the soldier, even if there is one or two pieces of content of another class you prefer. There are parts of the soldier I absolutely love in ME, wearing heavy armor and having medium armor from the beginning, but I fight best using the powers and abilities of the adept or the engineer, which means I lose the better looking (in my opinion) armor.
If there's a quest that needs a soldier's unique view, let the soldier have some dialogue that reflects that and adds content, but say we end up in a Grissom Academy like area, an adept would probably have a better chance to shine.