In the Mists of Pandaria Beta Classes Forum, Ghostcrawler replied to a comment concerning the new Glyph of Stampede:
The design intent is that Stampede skips over any unusable pets (such as an exotic for a non-BM hunter) or any blank slots (in the case that maybe you left a hole in case you tame something interesting along the way). For any skipped slots, Stampede would just clone your current pet for that slot, so you would still always have 5 pets when you Stampede.
The idea of the glyph is that it would use the clone mechanic all the time. Theoretically, a hunter with only one pet would be wasting the glyph.