MQ3D didn't change the enemy AI. At all. The game was just flipped and double damage was added (and the dungeons were different). So, in a sense, you're saying that we shouldn't have another Hero Mode, but that we should have another Hero Mode. Maybe you should clear the fog on you OoT goggles a bit.
Enemy actors were switched around along with the puzzles, so in a sense the enemy AI was changed. Clear the fog on your SS goggles; Hero Mode isn't a great addition.