Maybe we need a "NumpyObsoleteWarning" :) At the least, we should probably have a list of obsolete functions in the documentation somewhere. My main concern is that as we go forward we might end up supporting a bunch of functions that are seldom used and have better replacements. We need some method of pruning.
Given the list of uses Stephan turned up and Robert saying it's a useful function, I'm -1 on any warning. If np.diff gets the same padding behavior, we can document ediff1d in its document as being superceded with a recommendation to use np.diff instead.
To be clear, I don't think np.ediff1d is particularly useful or necessary, despite these uses. Most of these uses don't even use the optional arguments, so the author was probably simply ignorant of np.diff. This is more or less inevitable for most corners of NumPy's API, given how many users we have.
"PendingDeprecationWarning" is Python's built-in warning for signaling that something is obsolete but not deprecated yet. It might be appropriate to use in these cases. The default warning filters silence it for users, so it doesn't show up unless you're very aggressive about enabling all warnings.