Link's Awakening, the Oracle games and The Minish Cap had you to use your sword as an item from your inventory, meaning that you equip your sword with either the A or B button. The game automatically sets your sword to B when you get it, as if the game wants you to use the B button for it. The sword is always on B in the other Zelda games, so I see why. However, I prefer to have my sword on A when playing the handhelds. There are actually a few advantages and disadvantages with both choices:
A is the action button that you use to interact with NPC's, and if you miss NPC's while trying to talk to them, you'll just swing your sword. If your sword is on B, you might have items like bombs or seeds on A while doing this, meaning that if you miss the NPC's while trying talk to them, you'll just waste a bomb or a seed. Before you ask, yes, missing an NPC while trying to talk to him/her happens to me all the time.
While you're underwater, you can only use items with the B button, because you're swimming with A. If there are enemies in the water, you want to have your sword at B so you can kill them. However, with the Mermaid Suit in Oracle of Ages, you swim with the d-pad and dive/ascend with B, meaning that it's switched around, and you can only use A.
I think A is the best button to use because it's got more advantages and less disadvantages than the B button, and you can just easily switch your sword to B whenever you are underwater without the Mermaid Suit. Sure, if you use B for your sword, you can just switch it to A whenever you're underwater with the Mermaid Suit. However, switching the sword to A everytime you are talking to an NPC... yeah, you see where I'm getting at. Preventing bombs and seeds from being at the A button every time you're talking to an NPC is also pretty hard to remember.
A button all the way.