Require either a self link or an id as children of atom:feed elements. Don't require an alternate link.
Lacking an atom:id, the self link is the most reliable data to use as an identifier for a feed, making it a better alternative to atom:id than an alternate link.
Feeds may be the only type of internet resource that routinely have an alternate representation. While this convention arose naturally during the emergence of feed formats, no strong argument has been found for requiring this unique situation.
In section 4.1.1 of atompub-format-08, change this:
atom:feed elements MUST contain at least one atom:link element with a relation of "alternate".
atom:feed elements SHOULD contain at least one atom:link element with a relation of "alternate".
And add this bullet point:
atom:feed elements that contain no child atom:id element MUST contain an atom:link element with a relation of "self".
Tools which expect feed level links (such as Bloglines) will need to be prepared for the absense of this information.