The vast majority of FPS combat is fought on a plane...Even when you do find yourself in a situation where you need to aim above or below you, you're only operating within 180 degrees (ground to ceiling). Horizontal aiming, on the other hand, routinely operates on a full 360 degrees.
The idea is to develop a bounding box that fits that need. You'll need a box that is thin, so you'll start to turn quickly when you angle to the sides. You'll also do better with a box that is very tall, as vertical pivoting is rarer. The main problem with a large bounding box, after all, is that it hampers your ability to quickly turn around. Since aiming on the vertical axis isn't an operation that's tied to physical turning, you can still keep and benefit from a large vertical box.
A bounding box more grounded in reality
Using a thin box also maintains what I consider to be an important design rule for FPS games in general: the cursor should always be in the middle of the screen (horizontally).
In fact, there are quite a few circumstances when you'd want to keep your weapon centered on target, while at the same time glancing around to survey your surroundings. The motion-sensing functionality in the Nunchuck makes this desire a possibility.
Via a swift jerk of the Nunchuck, your character would turn their head to survey the environment. For example, a quick jerk to the left would cause your screen to pivot approximately 45 degrees in that direction, and then quickly pivot back. What separates this motion from a standard bodily pivot is the fact that your cursor, and the bounding box, would be unaffected. They would stay fixated on whatever you had them pointed at, while your view of the screen pans away from them momentarily. You'd also be free to move your cursor during the head pivot if you so chose, so you could quickly train your gun on a new target you noticed along the way.
If there's anything that should be easy to agree upon, it's that the bounding boxes being used in Wii FPS games so far are simply too large. While a simple shrinking of the box would definitely improve things greatly, I really do think that a tall and thin rectangular box would produce the most ideal results.