I prefer the speaker on the bottom, as it makes the most sense. If you hold the scanner, you do so from the bottom, not the top (unless it's upside down). At most, your hand is covering up the speaker which is the least objectionable of the speaker/keypad/display trio. Doing this, your thumb is right at the keyboard where it should be, and the display is clear of any body parts.
Now, IF they would put the speaker behind the display, and exit the audio out the top and sides, I would be fine with that. It would make the unit close to the size of the 396 again.
But, putting either the display or keypad at the bottom would be less desirable.