Marvel Studios President Kevin Feige explained why introducing the alien race of shape-shifters known as the Skrulls early in the franchise (in reference to the alien invaders in The Avengers) would be problematic for story-telling purposes, so introducing the Dire Wraiths - also an alien race of shape-shifters - would pose a similar issue. That is, assuming if either species were introduced in the live-action franchise they'd closely follow their Marvel Comics origins, abilities and unique designs.
Marvel is always looking far head and aliens are a big part of the franchise's future. Their involvement in Coulson's origins and return from the dead however, seems very unlikely. Equally unlikely is the idea of an alien being put in charge of an all-human black ops team.
Verdict: Shape-shifting aliens would offer a very interesting story come time for Phase 4 (or beyond) for the franchise, and would allow them to play with and alter the history of the films. For now, it doesn't fit and wouldn't serve the story of the show.