This was a very ambitious project for a first game! I'm not familiar with the plugin you're using, so I can't help much with how to edit the damage formula, but as for telling enemies apart - perhaps some colour coding would help. You referenced fire emblem as an influence, and in those games, it's very easy to tell ally and enemy units apart since allies are all blue and enemies are all red. With larger sprites, using that sort of system might look strange, but having some standard colour coding between the two sides would be beneficial.
I think the comic book style cutscenes - regardless of your skills as an artist - would have been really cool! :> But with the time limit and you learning RPGMaker MV at the same time, perhaps not the best choice with the time limit.
Keep up the great work! I wouldn't have guessed this was a first project - didn't even encounter any bugs ; )
Invincible Pepper Squad for the win!