Should the new protagonist acy in a style similar to the paragon/renegade system like Shepard did, pr not? I spend some time reading posts from fans of Mass Effect and Dragon Age (without delving into unrelared spoilers) and we "complain" on how our characters act. Such as the character being too brutal or not brutal enough etc, I recently started watching Firefly after seeing the movie Serenity and took some inspiration from Mal (main character).
I found the character to be quite different among the "classic" heroes, as Mal portrayed a man not trying to be a hero, He was his own person, a Renegon if you get my meaning on that term. I am not saying the new protagonist should be like Mal, but take some inspiration from the character.
Extract from Wikipedia: "the character Malcolm Reynolds was the only definite character he had in mind when formulating the ensemble cast. He wanted a hero, but not a hero in the classic sense; someone that is "everything that a hero is not.".
It is hard to make sense of what I am trying to propose, but I hope we have the option to show a brutal and dark personality but within reason. And I do hope we do not get roped into a ME3 style of Shepard's behaviour showing forced emotion of regret and such which some of us prefered if it was an option to choose wether to express regret or a not-caring attitude.
Mal is a reluctant hero. Characters like that are actually my favorite sort of hero. It isn't that they are "paragon" or "renegade", but that they don't WANT to be heroes. They have their own plans, their own lives, but ordinary people placed in extraordinary situations can sometimes rise to the occasion and be extraordinary. That's Mal.
That wouldn't work for Shep or a character like him for a lot of reasons. First off, he is a space marine, and a reluctant hero personality wouldn't work. He is a warrior and a protector by trade. Secondly, he is an avatar of the player. More control over his personality should be granted to the player via dialogue options.
But, those dialogue options should not be "paragon" or "renegade". It forces a black and white, infantile and simplistic view of morality on the writing of the story. That's why my Shep inevitably ends up paragade. Sometimes, choosing a paragon option is correct, and sometimes choosing a renegade option is correct.
The ONLY way a background personality like Mal would really work for an otherwise blank slate protagonist would be if the main character was not a space marine, but instead a smuggler, mercenary, explorer or similar type of character who just wants to do what they do without being the savior of the galaxy. Such characters are particularly good when they actually resist rising to the occasion and saving the day, but ultimately do so anyways. It makes them more human. More relatable.