Condensed from OP's post
Something that irritates me ... is the notion that the 'PC' should be the most important, successful and idealized role in the game... if everything is a reaffirmation of how great the player is. Sometimes the protagonist is downright Gary-Stu/Mary-Sue like because they have zero flaws, accomplish everything and all their cohorts just stroke their ego...- it becomes too much, and characters aside the protagonist diminish in importance or competence in the story.
For example: What if people were skeptical of him? What if you're confronted by a squadmate telling you "I think you're obsessed with this, what drives you to do all this?" [This begs the question of] who our character is as a human being. [This] adds depth to it and ... another sense of gratification that feels genuine.
There's nothing (worse?) than the sense that you're always doing good by completing objectives and then have NPCs tell you that you're amazing for it. By having addictive gameplay objectives and making the NPCs question the actions of the player you're enhancing the link between gameplay and story and it makes the characters feel more grounded and realistic.
More importantly, you can't have a good character if he has no flaws, and ... it means doing something incorrectly and being oblivious to it, and that makes the character human because humans are fallible and never perfect.
What do you think, and do you agree or disagree?
OP, I think you are making a good and novel point about having a PC's character/personality have a 'flaw' that can become an integral or recurring 'more realistic' aspect to the PC's attitudes and the outcome of their encounters throughout the game. As we see the PC's flaw wane and improve over time, we can begin to root for them even more. Understanding a character's 'flaws' can meaningfully help us understand the context of their personal background more completely, and what makes them 'tick.' I want to know more about my PC than just their drive to save the galaxy at all costs. We can become 'invested' in our avatar's personal development, in addition to improving their combat development through upgrades, and, rather than playing a homogeneous 'I'm always the same person from beginning to end.' Note: Players have commented that they liked shaping their Shepard's personality from starting out as a renegade to becoming a paragon type. This is a good argument against tying P/R points to the PC's capabilities or blocking dialog choices later in the game, imo. Let us see our PC grow as a character through the interactions they experience in-game. Does the PC ever question him/her self? Or even their attitude and decisions with the squadmates? Liara: "Shepard, why did you do that?" Questions should be asked of the PC that reveals them even further.
If the Protag has an obsessive character flaw, and it is spoken about by squadmates, fellow travelers, civilians, at alien encounters, etc., can it be useful as a character and story element? I'm thinking, like the OP, that it can make us more curious about the PC's background: "What is driving them so hard?" Where and how did that obsessive flaw originate?
Note: I would have liked to have seen Shepard talk more about their personal experience as a colonist, spacer, and earth-born that influenced their way of thinking and decisions in dialog choices. It seemed to me that Shepard's personal background made no difference - his/her attitudes and available dialog choices were homogeneous despite their optional backgrounds. How would Shepard have spoken or expressed their viewpoint in dialog options, considering their past as a colonist, or a spacer, or earthborn? Did the A. and C. dialog and D/E Persuasion options have to be tied to their Paragon or Renegade style? I might say something differently if I was a colonist and not earthborn, referencing my past personal experience as a way to handle a tense situation: "On Mindoir, I ...." The character's 'flaw' could offer similar alternate dialog choice possibilities rather than either 'I want to be the nice one, neutral, or the bully." I'm not knocking ME - it's a brilliant game and story despite it's minute or so-called 'glaring 'flaws'.
In ME-1, Ashley's character was highly criticized by some for being a bit 'racist' - her 'flaw' in distrusting aliens. I viewed her early 'alien-cautious' attitudes in ME-1 as an interesting alternate viewpoint for a character who had a very different human background, and not as a blatant racist in her character; especially not given her family's personal tragic experiences during the FCW, and with her having a limited experience in not working much with aliens in the Alliance and through her colonial tour duty experiences prior to meeting Shepard and the geth on Eden Prime. After all, she was stationed on Eden Prime to protect the colony from alien slavers and pirates. But Ashley's character 'flaw' grew to become far more accepting and trusting of her alien squadmates, growing with experience and time, and Shepard helped her to see the bigger picture and mature in this regard. Note: In ME-3, Ashley referred to Tali as 'kind of like a sister' if MaleShep changed romance interests from Ashley to Tali.
Ashley's so-called 'personal flaw' is a truer narrative and a contextual reality of the human experience - the personal growth that occurs in the course of seeing and experiencing situations that one hasn't had before. Mark Twain's Huck Finn changed his attitude (and ours) about black racial stereotypes in his journey down the Mississippi River with Miss Watson's slave, Jim. What if it was Shepard was forced to work with the aliens he'd never trusted before? Ashley's personal 'flaw' narrative served the reality function that not everyone had mentally or emotionally gotten over the loss of life and tragic circumstances due to the First contact war - only 20 years earlier. And - she was absolutely correct: Many of the aliens (including members of the Council) didn't trust humans either. So, were the aliens' anti-human attitudes racist too? Where was the fan outrage over their comparable 'racism' to humans? Non-existent. That leads to the story problem where humans think they are better than aliens.
As I've thought about your OP comments, they got me thinking about how a PC's obsessive flaw could be addressed in the course of completing the plot, and ways that conversations would reference it during the course of the game.
Q. Is the PCs obsessive flaw something that makes the PC more successful, or less successful?
Q. Does the PC's personal obsession achieve a cathartic (or therapeutic) healing at the ending climax of the story arc?
Q. How does the PC react to the other characters when they are talking with the PC about their 'flaw'.
Q. How would the PC react if they entered a room on the ship where their squaddies were talking/grumbling about him/her in an unflattering or critical way?
Q. What if the PC's flaw caused a squadmate to leave, or it caused a squadmate to turn against him/her?
Other ideas?
OP, a corollary to your question: Do you think it is unrealistic and boring that the PC is always successful?
It can and does for me, at times. I'd rather have some mission setbacks, or mission failures, and eagerly anticipate how my character is going to handle the next encounter to defeat them (Like Kai Leng, and facing off with Saren at Virmire, and Saren escapes)). I also wonder how it would feel to me if I chose the wrong squadmates for a mission, and it would end in a mission failure or a squadmate's death (eliminated from the game entirely), where I didn't make a mission choice like on Virmire as to who would live or die. In this scenario, I would be utterly stunned that one of my squadmates had been eliminated from the game. This is why Mordin's loss at the tower was a very moving ('feel') experience for me. Either my squad is reduced for my playing future missions, or I'd have to replay the level with different squaddies to achieve a successful outcome with no squadmate deaths. Perhaps a squadmate is wounded and has to play wounded for the rest of the game. As it is, I can successfully complete any mission regardless of who I choose for my squad. It's a bit boring in that I already know that I will be successful regardless of my squad choices.
Q. What if, in the course of the battles in Andromeda, the PC loses as many battles as he/she wins? What if the very ending of ME:A leaves the Protag in a draw, a stalemate where this is no resolution (yet) - and the final confrontation will not be decided until the end of the second or third game? A cliffhanger? And... if it's related to the PC's fatal 'flaw'? Would you say that you are going to be 'satisfied' with an unfinished story? This is also a possible reality - not winning for a while over several episodes. Comic books, like soap operas, leave you hanging with the 'what in the blank is going to happen next' limbo - feverish for the next installment. How long would you be willing to go in a game if the penultimate boss defeat did not occur until the end of three episodes? For me, it would depend on how many years it would take BW to complete the next trilogy. I might prefer to play a series of DLCs that were like a comic book series issues, where each DLC progresses the main story a little further each time. Each DLC is spaced out every 3-6 months or so for several years, instead of having a slew of DLCs released within a few months of the game's initial release that are only another mission in the current timeline. I need to think a little bit more about this.
I'm interest to read additional serious comments on how a character's 'flaw' could add to the interest in a ME game.
What character flaws do others of you think would make ME:A more interesting?