Recently I submitted a comic book story to a publisher, and they criticized that the main character is basically just a shonen protagonist (for example, Son Goku from Dragon Ball, Ash from Pokemon, etc.) in female form. They're interested in keeping the character female, but suggested that I should put more emphasis on the female aspects of the character, to make it more distinct from the average male shonen protagonist. How should I begin doing that? (note: I'm a man)
Consider how the world reacts to the character
Fundamentally, female characters aren't that different from male ones. The key difference is that women are treated much differently than men are, and as a consequence the way they see the world and how they move through it can become very different from how men do so. (If you don't believe that people treat men and women differently, here is a fairly simple example).
So one way to approach writing female characters is to consider how the world will react to their actions, and how they will change as a result of those reactions (which of course stretch back to infancy). This can be tricky for a male author to do, because we don't have the same set of experiences to draw on.
The best way to get around this handicap is to read. Specifically read women authored by women. If you can't experience the world the way a woman would, the best substitute is to put yourself in the shoes written by someone who knows those experiences by heart. Pay attention to how those women are treated by the world, and how they respond to that treatment.
My personal recommendations are The Calculating Stars by Mary Robinette Kowal and Middlegame by Seanan McGuire, but that's only scratching the tip of the iceberg. There is no singular "female experience", only a shared pool of similar interactions, so your best strength will come from reading widely and broadly.
Well, do you have any female friends you could ask to review your writing? other than the genuine feedback that only a woman could give you, you are hardly the first male writer who is trying to write from a female character's perspective. You could try reading the works of male writers who had done this pretty good and read their books with a writer's hat. A good example of such author I could give is Brandon Sanderson. Notable female characters: Shallan from the Stormlight Archive, Vin from Mistborn, Sarene from Elantris, and Spensa from Skyward (among others of course).