The Shuffle is the base pattern for a type of throw called
the Slam. It involves raising your hand up and forcing the ball diagonally
towards the other hand, similar to the horizontal passes seen in the Shower.
This type of throws feels good to juggle, and looks great to an audience.
Breaking the pattern down, we can see that the Shuffle is actually very similar to the Shower (they even have the same siteswap). The only difference is that instead of making the horizontal pass underneath the pattern, the Shuffle makes the pass through it (Slam throw). Knowing this, it would be best to start out by learning Slams. Start with one ball in each hand. From your non-dominant hand, you are going to throw one ball across your body. Then bring your dominant hand down on top of it, throwing the ball currently in that hand downward to your non-dominant hand, and catching the first ball:
Practice this a lot! The throw will likely feel very weird at first, but you will need to be comfortable with it in order to juggle the Shuffle. For the next step, you are going to use three balls—one ball in your dominant hand, two in your non-dominant. Throw one ball from from your non-dominant hand, and wait for it to reach the peak of its path (like in step one). Then, you are going to throw the second ball in your non-dominant hand, and then immediately after you are going to make a Slam throw with your dominant hand:
Like many other tricks, the Shuffle is all about timing. Practice this second step until you you can perform it smoothly without dropping. After that you simply keep adding in extra throws. Start with two, practice, and then move on to three. Gradually—and I do emphasize the word gradually—you will start being able to run the Shuffle longer and longer. It is also worthwhile to learn the Shuffle using your non-dominant hand, as the Slam throw is used in tricks that require both hands.