The existence of well written characters does not excuse the truly terrible sections where the story forgets the vast majority of options available.
Just because Shepard can't be bested in one on one ground combat, it does not make him running on to a spaceship (which has proven the only thing which can kill him) any less of an incredibly stupid idea.
There was absolutely no reason for Shepard to die at all, but for some reason it got stuck in to artificially jump-start the plot and make the tacked-on RPG reset to level 1 make sense, even though it never impacts the plot in any meaningful way later on.
Why in the mother of god, when Shepard's entire overt mission is to rally the universe against the threat of the Reapers, does he leave the biggest piece of evidence and then destroy it for no apparent reason besides superstition.
Why is saving technology which could reveal the secret of 50,000 years of history and extend the scientific knowledge of all the races of the galaxy considered the evil option, whereas blindly destroying it for superstitious reason is the good option?
They've mentioned several times that Mass Relays have to be activated to work, so can they deactivate the Omega-4 and solve all their problems, or how about mine it? They expressly mention that no one uses it anymore besides the Collectors. No, because that would solve the plot and end the story, so we never mention it.
And as your point with Star Wars, would it have made any more sense if Luke had been killed in the first 5 minutes of episode 5, and then reincarnated him due to the force at the ten minute mark?
Well written characters only help you flesh out the universe, they are no excuse for massive gaping plot holes and scripted pseudo-choice nonsense.