Key sentences:If I remember correctly, the plot in the game revolves around a girls' sports school (or university), and the episode you mentioned is related to a girl who practices martial arts. It's not surprising that she was able to strike the MC. In such circumstances, she may seem stronger than him or be on par, but it doesn't make the main character weak. That's my personal opinion. And it was just one episode throughout the entire game. Not all girls should be angels seeking male attention; there should be bold, independent characters. I'm a developer too, and I think this adds interest to the game.
"girls' sports school (or university)" - yeah, SO? MC is weaker, writen as weakling then.
"a girl who practices martial arts, It's not surprising that she was able to strike the MC" - yeah, my point exactly! MC a weakling.
"she may seem stronger than him or be on par" - Meaning MC maybe weaker and deffo NOT stronger, MC a weakling.
"but it doesn't make the main character weak." - all the above? YES it DOES!
"I'm a developer too" - No disrespect, but... Soooo? that doesn't mean you are a good writer or know how to write a strong MC, sorry.
"and I think this adds interest to the game." - No, not really, at all! but you know what maybe will? MC one hand catches and stopped the loli's attack without breaking a sweat and facial change, then accidentally threw the loli half way across the hallway coz of muscle memory reflex. pretty sure that'll add a hint of mystery to MC as well.