I'd definitely remove Passives in battle.
I also prefer to have Skills/Spells above Guard/Defend, as Guard/Defend is less useful.
I'm also not sure why you can't have Skills & Spells in the same command mixed in. The Disgaea games do that without any problems.
It's because of your sprites. Open the image in an editing program that has grids (GIMP is free if you don't have any), set the grid to 48 and you'll notice how it cuts off the bottom row of your sprites each time.
If you move the image up one pixel, the problem should be gone.
Is there anyone who would like to resize some of sprites I've got and put them into MV sheet? I'm bad at that kind of things. I want to make a game, but I lack in resources and I'm bad at recolouring them, so my only option was to use a sprite maker from one game (Ive got permission to use it) but these are sprites from VX Ace and I only have MV. So, is there anyone interested in helping me?