From Adam Prosak (lead developer of Eternal Masters):

With our main sets, commons serve as the backbone for limited play, and we put most of our attention there.  We allow for commons to be constructed cards (usually Standard or Pauper), but our focus is on limited. 

With reprint sets such as Vintage Masters and Eternal Masters, limited still plays a primary role, but we do keep pauper in mind when making the sets.  Usually we will do a pass on all of the cards that have been downshifted to common to make sure that we are happy with the cards we are downshifting.  For example, Nimble Mongoose, Elvish Vanguard, and Yavimaya Enchantress were all included to make their respective archetypes work in Eternal Masters limited, but we were also happy to either create or improve an archetype in Pauper.

Finally, due to how our schedules work, Eternal Masters was finalized before Cloud of Faeries was banned in Pauper.  I think that if I knew that we were going to ban Cloud of Faeries in Pauper, I would’ve been much less likely to include Peregrine Drake in Eternal Masters.  I believe that Peregrine drake is weaker than Cloud of Faeries, but both cards lead to the same degenerate combination with Ghostly Flicker.