No developer has tried something like this, but, what would work:
When you begin the game, you get a menu and choose whether you'd like a lot of customization and interaction or not (There would need to be more depth in the menu but that's the gist of it).
Those that chose all the customization and option (dialogue, loyalties, etc.) play the same game as those players, which chose the 'dumbed down' version but instead of just cut scenes and basic interaction with npc to receive missions, etc, more menus and interaction become available.
IE> Character Development: May be setup to have a choice of increasing either stamina, strength or tech one point per level and choose to increase biotics, weapons or tech another point of that level. OR You can have more detailed menus allowing players to micromanage small weapons, sniper rifles, tech, etc. The latter allows for fine tuning while the first option allows certain automatic ups of these sub-skills based on the broad selections.
IE> Interaction: Basic players can be led around with map markers and have short (right or wrong, help or deny) quests and most side quests can be outright ousted. Players wanting a more immersive experience would have all side quests open and more dialogue options.
Consider that the above is already done albeit on a smaller scale, in many games (for instance, some rpg's allow certain interactions with npc's based on your characters skill level in a particular area - this shouldn't be that difficult to transition to the above).
IMHO, the first developer to do this will score unprecedented sales of their IP.