...but to me, you've basically admitted that you didn't think about any of this stuff before I brought it up, 'cause you basically just regurgitated everything I said and called it "fleshing out the character". Which, fine, that's better than nothing, but I'll get to the new logic issues that this brings up.
See, here's the thing I need to mention that points to a larger problem here: to my mind, you've confirmed that it's not an issue of "I have fleshed out the characters and I just have difficulty writing that", as much as it is a case of "oops, I didn't think that far ahead". See, that right there is the reason why Rule of Cool is such a problem in badfic. Badfic authors constantly think "well, how cool would it be if this character was this or could do these things" without thinking about them from a logical standpoint within the context of the story they're in. As such, things happen that make no damn sense.
My classic example? Parallel Realities, which was a terrible Mass Effect fanfic which involved some stupid AU where Commander Shepard was a not-human alien from another reality with its own set of aliens. Now, Shepard constantly tells us in that fic that his galaxy can't reveal themselves because "dude, the Council would subjugate us 'cause we have all this stuff". Problem is, the author then decided "hm, I should let the Rule of Cool apply to these alien races and make them as badass as possible". So later in the fic, you were seeing their ships do things like take out an entire batarian slaver fleet, and take out four Reapers with one shot. They mention that their numbers are too low, but their technology is way advanced to make up for this. The problem there is that it ruins any credibility Shepard had, because the fact that they can take out four Reapers with one weapon indicates that they would in fact have the technology to not be subjugated by the Council. Because of the Rule of Cool, the author of that fic invalidated his own main character's reasoning for not doing something pretty significant, and as a result a large part of the plot became rather stupid (not to mention that it made it obvious that the only reason they weren't intervening was because there would be less plot regurgitation that way).
That's the kind of thing that unchecked Rule of Cool can do to a fanfic. And from what I'm seeing here, you're currently in that same mindset. I appreciate the enthusiasm, but you need to slow down and really think about the characters and their backstories before doing stuff.
Okay. Back to the character.
Now we have new problems that're brought up. So he was given drugs to repress his memories? Um... pardon my vernacular, but you do realize how ...ed up that sounds, right? "Oh, he's a problem, but that's okay: just throw some memory repression drugs at him and it'll be all fine!" I'm pretty sure it doesnt work like that: what if he's resistant to them? What if he goes off his meds for even one second? Wha then? And on top of that, memory repression drugs do not work like that in anything that isn't To The Moon. Granted, Medical probably could come up with something like that, but someone in Persona? Um, no. I doubt it, nor do I think that the suppression of memory would exactly be the right solution to his issues. I would say more, but I'd have to bring in my friend who's currently getting a degree in criminal psychology and I really, really don't want to drag him into any more discussions about badfic psychology than I already have.
Second of all, you've just made Nagi overpowered with the Wild Card. I'm not sure you understand this, but the Wild Card is a protagonist-centered ability, and said protagonists are said to be special by the canon. So you see, even in the canon they know it's unusual. By the very nature of Wild Card as a special ability, you're making your character speshul in a way that few canon characters would be. It doesn't matter how much you neuter his ability, it's still special according to the canon. This wouldn't be as bad if this was the main character of a different group that had nothing to do with anything related to Persona 3 (as well as any of the other Persona installments), but the fact that it's dealing with Persona 3 just makes this worse for me.
And for the record, the only one who has Wild Card is the player character himself (and Aigis in "The Answer", but for her it's an even more special case considering that she loses an ability she had in the main game to get Wild Card). All the other members of SEES get one Persona that evolves as the game goes. Their Persona evolves into another one, but they still only keep one Persona. You may notice that this is NOT the same as being able to summon multiple Personas. Therefore, I have no idea why you said "protagonists", plural.
Third: So if Nagi had never been given meds, he'd be exactly like your other character? I guess that's good to know that we're dealing with two of the same exact character here.
Fourthly, what good would a biotech parasite do to keep a Persona from killing him? Personas function through willpower: they're manifestations of the personality of the characters that unleash them, and it's revealed in "The Answer" that the Personas are tamed Shadows. The reason they went with drugs in the canon is because psychiatric drugs in the real world affect how the brain works. How would something that works on the body help control a matter of the mind?
And lastly, branching off from the above point: the reasoning of the above point is probably the deal breaker for me, and I'm sure it would be a deal breaker for any PG here. To me, this tells me that you don't seem to understand how Personas work. Let me repeat that: this tells me that you don't seem to understand how the Personas--the things that make the entire plot possible, the things that get tons of exposition for, and the things that make up the frickin' name of the frickin' continuum--work in the canon. This right here is the most damning thing to me in terms of everything you've written down. Your character is written in such a way that it disregards how Personas work in the canon, which means that it's a massive canon violation. And frankly, it doesn't matter if you do know how Personas work: it still indicates a lack of thought on your end. If your attempt to "flesh out" the character involves completely breaking the most important part of the canon, why should we trust that you'd have the judgment necessary to be able to give an accurate assessment of the problems of various badfics in any continuum?
Now, I'm not a PG, so someone else may see this differently, but if I were a PG, I'd tell you to take it all back to the drawing board and start over. Frankly, I don't think you're ready to write for the PPC in any capacity.
But you know what? That's okay. Not all of us in the PPC write missions. Most of us are here to learn, as well as to make fun of bad writing. I do think that the character here exhibits some major Gary Stu tendencies, but I can tell that you're passionate about writing nevertheless. That's a good thing: now all that's left is to filter that passion so you can do it right. And that can be done by slowing down and not jumping into things.
The creative process is not something that happens instantaneously. It needs to come at the right pace, and in this case I think the right pace will come from you slowing down and thinking a little more about what you want to write.
