I can see a use for multiple wish lists.
For instance, I mainly get books from Amazon UK, but occasionally, for myself or as gifts, get them from Amazon US, and could do with two separate lists. Others might want different wish lists for different family members.
There are a couple of obvious work-arounds. One could create a new collection, excluded from the library. Or one could use a custom column (of which there are plenty in the betas and so in version 4) to distinguish as needed.
But they are work-arounds, not as neat as multiple wish lists, though possibly good enough that it isn't worth changing the program to acommodate multiple lists.