I don't know if you have ever seen a subwoofer but in order for them to work you must put them in a subwoofer box (resonating chamber) to achieve the best possible, loudest, sound. Now you can still use the sub speaker outside of the box and you will still get a decent sound, however it becomes more dependent on the surroundings verses the one in the box.
In this case, the speaker in the 12.9" iPad Pro has a resonating chamber behind it, much like a sub in a box. This increases the sound output, quality, and depth. All four chambers are the same size so they are able to adjust the sound output depending on the orientation of the device.
iPad Pro 12.9" interior, showing the large chambers behind the speakers:
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This explains why the Pro 12.9" can achieve such a deep spacious sound compared to other devices. The only reason it's louder really is because the speakers themselves are much louder. The resonating chambers don't increase volume dramatically past a certain point.
The iPad Pro 9.7" however doesn't have the space for these large chambers so the speakers are essentially the same as the iPad Air 2. The major difference is they are different sizes than the ones used in the Air 2.
iPad Air 2 Speakers:
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He is pulling the right speaker in the image.
iPad Pro 9.7" Speakers:
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You can see them on the left and the right, the left being the top of the device and the right being the bottom of the device. Very much the same style as the iPad Air 2. This explains why they can't produce quite the same sound the Pro 12.9" can. I have used both devices now extensively and I can tell you the sound on the newer iPad does not compare to the 12.9" Pro. The larger iPad actually produces much better sound than many laptops I have used!
Hopefully this clears everything up.