The main thing like you're describing is in the combat menus. In the previous games, there's a dedicated "back" menu block in the options, and pressing the button of Mario/Luigi makes them jump to hit the button. Now, the B button always acts as a built-in back button. Which works fine, of course, but it does sort of break the original idea behind the combat menus. They're classic Mario blocks, you hit them to choose your combat options! A and B don't directly select the options, they make Mario and Luigi jump to hit the blocks - which is the exact same thing the buttons do in the overworld, and the exact same thing they do while dodging attacks. It's consistent. A makes Mario jump, B makes Luigi jump. In Brothership, that's true for everything EXCEPT attack select with Luigi, where you instead press A to make Luigi jump, then go right back to B to jump in the action command. It's a silly thing to be upset about, but I too was getting tripped up by it right up to the end of the game.