@holysmokes762 asked: How do you ensure that your MC/reader character doesn't become a Gary Sue? More specifically, how do you write such a story without making the character the focus of the universe the character is in while the main story is still going on (MHA for example)?

So, when you say Gary Sue, I assume you mean a Mary Sue, or a character that has no flaws. Well, the interesting thing about my writing process concerning writing characters, is that I write my characters centered around their flaws. Remember that I say that character development is the core essence of a story, and good character development often involves acknowledging and overcoming flaws. Such self reflection is important for change, and that's what characters are supposed to do, because that's what people do. People change. 

Since you mentioned my My Hero Academia story, I will use this as a reference. When I first began creating the MC for that story, the first thing I knew is that I wanted them to be different. Different from the other characters in the universe of MHA, and different from the generic "I want to be the greatest hero in the world" character that essentially every other MHA fanfiction features. So how do I do this? Easy, make him the exact opposite. Instead of having a desire to become a hero, what if he were opposed to the idea? Then plopping this character down in the middle of a world where society basically worships heroes, and in a story where the plot revolves around young people training to be heroes, already creates an interesting dynamic. 

Next I asked myself, 'why doesn't the MC want to be a hero'? Well, at a basic level this is difficult to write, because what kid doesn't want to be a superhero when they're growing up? So then I have to really evaluate the character I'm trying to create. Is it that he doesn't want to be a hero? Or is it something else? I looked at Koda from Season 3, who didn't like heroes because his parents died because they were heroes. The real underlying cause was a sense of abandonment. And really, all deep rooted hatred of something comes from an underlying condition. People aren't born afraid of the ocean, there's something psychological that causes that fear. So what is it in MCs past that makes him hate heroes so much? Asking these questions lead me to the character I am writing today. His hatred for heroes isn't towards the people themselves, but towards what they represent. They represent people who use their quirks in extreme ways, and even if that is to protect others, it's something that MC resents, because he himself has no control over his quirk, and that in turn has caused him to hurt people. So his problem isn't with heroes, that's just him projecting his own personal issues onto a physical embodiment. And giving form to the things you resent makes them easier to hate.

In summary, flaws are what make people. Mary Sues aren't interesting characters. If you're still having some trouble, try following this outline. Person wants something. To obtain something person must do something. In this, person is the character and something is their original goal. The thing they must do is the story, the journey. But after doing something, person realizes that the something they wanted is no longer what they want, or what they need, because in doing something to obtain their goal, they have changed as a person. It's a very common and very effective outline used to generate great character development and even greater stories.

Another thing is this; don't make your characters overpowered! If you do that, there's no conflict. We call this the Superman phenomenon. Even though MC in my MHA story seems like he's unstoppable, I place restrictions on him. He's afraid to use his power, so he's limiting himself. There is an internal conflict. There are other ways to deal with the Superman phenomenon as well.

I would highly recommend watching "Ip Man: How to Write Superman" by Accented Cinema on YouTube for an in depth analysis about this issue. I also strongly suggest watching the writing tips series from Hello Future Me.

If you really want an in depth look at my creative process though, I'm going to be starting an Attack on Titan fanfiction soon, and will be writing a book alongside it that walks everyone through the thoughts I have in my head as I go about creating the story.

As for your second question, how do I write without making my character the main focus of the universe? Quite simply I understand that they are not the main focus of the universe. So many fanfictions in the reader insert genre have an overpowered reader character, and I find that is the main crux of the issue. And that's perfectly fine if you want to write it that way, but I find it creates a rather dull story because there's no real conflict and no real threat. I just remind myself that my character, though contributing to the story, is not the main character. They're the main character of my story, but the not main character of the story, if that makes sense.