Thank you for the comments. I understand everything you said from combat and story. First I want to say that I didn't know how to use RPG maker MV and how to change damages, HP and other things.
I noticed one of the Pepper squad member didn't take a lot of damaged. When it came to enemy aggression, I don't think that is something I could fix sadly, in fact the "Tactical Battle System" plugin the game is using is limited on what it could do. The creator of the plugin is planing on adding new features that will improve the system, but as of right now there is nothing I can do, especially with a "skip turn". That was a pain I understand. I could fix the range of the guns, they did added a feature for weapon range but I couldn't figure out how to work it properly. I did change the sprites to differ enemy from allies, but will check into it more in the future. As for the story, Yeah it's really dumb, (It was an throw away idea I had a while ago.) Originally, instead of the stationary "cutscenes", I wanted to draw pictures comic book style, but I was using MS paint and every drawing looked like a first grader drew it. It was also putting a lot of stress on me. I will defiantly work on the story more and improve on storytelling.
Thank you for the comment again and I will improve, this is my first game I had made (and was working alone) so I expected not to do so well.