Now that I look at it, it's a bit odd how the battle commands work. Rather than using the perfectly valid built-in controls, it instead made the new def pbNextIndex to do the exact same thing.
Actually, it's probably a remnant from an older way it used to work, before it used Window_CommandPokemon. I'm not sure how it all makes sense, as it appears that both ways are working at once.
Anyway, try this:
The only downside to this is that this also applies to the fight menu. If you wanted that to be a straight list too, then problem solved, but if you wanted it to be 2x2, you'd have to do something extra to keep it the way it is.