To be honest, Chrono Trigger has a similar narrative structure. At one point you can freely tackle Lavos through multiple means...but should you?
The whole point is that the big bad isnt going anywhere and its up to you to prepare your characters, complete their arcs, make them stronger and get better equipment to slay this beast properly.
Hell, Mass Effect 2 technically had this too. You could tackle the collectors but should you? Do you feel your crew and ship are ready? You are their commander and whatever happens is on you.
Yeah, its not perfect for everyone but I dig it...gives the player a sense of control and exploration.