In a recent exchange with an editor, I had to choose between "What matters is the [singular version of phrase X]" and "What matter are the [plural version of phrase X]." My first reaction to the latter option was, "Huh, sounds strange."
Now sometimes sounding strange is good: For instance, it's often good to use less familiar (but apt) imagery -- imagery which is "strange" in the sense of less familiar -- than familiar and therefore cliche imagery. The fresh imagery is more likely to capture the reader's attention, and to convey the message.
But you don't want to focus the reader's attention on a routine transition like "What matters is"; it's therefore best, I think, to phrase such routine items in routine ways -- to use common versions, not strange ones. (Other writers may legitimately disagree, but that was my judgment for my piece.) Yet was I right that "what matter are" is much less idiomatic than "what matters is"?
Google to the rescue: Google reported for me 400,000 results for "what matters is the," 35,000 for "what matters are the" (which I think is grammatical, but for reasons I don't want to get into here), and fewer than 1000 for "what matter are the." Matter settled.