I'd also like to just add some rationale behind the B-as-navigation-key approach.
The fundamental issue is that a NES controller is 3cm wider than a Gameboy and it's also ergonomically different because of the shape. One key point is that on the Gameboy, with the unit in a 'normal' position in your hand, it's pretty easy for most people to reach over with their right thumb to hold down SELECT. If you try to do that on a NES controller, it becomes awkward and most people I tested it with (granted, not people that use LSDJ), they tended to have to shift the controller in their hand to make a navigation move using SELECT.
With B, the key is right there under your thumb and anyone can comfortably perform the move. My approach, therefore, was to make all the most commonly used functions as comfortable as possible (OK, it doesn't always work) using just your two thumbs, without having to move your hands from the 'standard' position or end up having to grip the control in one hand and use your fingers on the buttons.