Protagonists, despite their central role in an anime, very rarely make or break stories. As opposed to many other forms of media where the protagonist's personality is the driving factor of the plot, many anime do not rely on their protagonist to keep the story interesting. I believe this is because so many anime nowadays have shifted their focus to secondary aspects of a story. These being things like comedy, action, and world building. Don't get me wrong, those aspects when done well can be a fine basis, but that's no excuse to leave a protagonist bland and undeveloped. You can't just skip a crucial part of writing because it's an anime, and several shows are worse off because of this laziness.
One reason to choose a protagonist for a story is to explore a set of values. Anime can serve as an examination of a person's values by having the protagonist have firm beliefs, just for those beliefs to be challenged. Both Fate/stay night and Fate/Zero are prime examples, using the violence and scheming of the Holy Grail War to question the beliefs held by Shirou and Kiritsugu respectively. They both want to work toward a more just world, and one sees the war as a means, while the other sees it as an obstacle. A protagonist must have values in order to analyze them in a show such as these, so having a bland, self-insert protagonist removes any possibility of exploring a value system.
Another reason to write a certain protagonist is to explore another idea from a specific perspective. This is how shows like Log Horizon and Higurashi no Naku Koro ni function. In the case of Log Horizon, the show is about how a group of gamers would approach the task of running society. Higurashi is about (to some degree) what would happen when someone tries to solve a difficult mystery despite being a paranoid kid with a history of being suspect. This type of show prefers to focus on its secondary aspect like I mentioned before, but rather than leaving the main character by the wayside, it utilizes the character to both explore the themes more profoundly and to explore the interactions between said secondary aspect with a protagonist willing to react. One of the best examples of this that I can think of is Fullmetal Alchemist for its world building, and how alchemy shaped the lives and ambitions of the Elric Brothers.
Despite the choice of main character being such an influential aspect of a story, many anime seem to get away with taking the easy way out. These stories feel more like a world exploring itself on autopilot, or maybe it feels like senseless action. No matter how it is done, the result ends up being a bland story based solely on its premise and scene-to-scene execution. Entire genres of shows can fit into this category, including slice of life and most isekai anime. This is not to say that these shows are bad, but they have untapped potential that usually can only be alleviated with a solid secondary cast, which even so, is just a roundabout way to solve a simple problem.