Morbi
Scavenger
What a great question; in order to accurately answer the question, we must discern which interpretation of "deserving" you are alluding to. I will presume that you are referencing the notion that he is not the most prominent character (appearing in only one game), as indicated by others. However, @Do you personally believe that Dark Pit is deserving of being in Smash 4?

So the whole, "Medusa appears more than once, she is more prevalent and thus more likely" argument is utterly arbitrary. Not only that, but most would expect Medusa to be her own character, correct? Same goes for Hades. Few competent people want a completely unique character that offers something diverse to be forced into clone status when there is quite literally a clone within the series.
Does he deserve to be playable? By merit of Sora Ltd. developing the game and not yet adding one of their own characters, I would probably assert that Dark Pit does deserve it. He deserves it over another Donkey Kong character. Series importance is not relevant in the slightest. If it was, the entire roster would be Mario and perhaps a few Pokemon. Maybe, just maybe, Link would make it in the game. It is a cross-over game and Kid Icarus is treated as a front-runner series. Each main series has a semi or pseudo-clone except for Kid Icarus. So it would not be unreasonable for a series to jump two characters in one game. Apt precedent serves to illuminate that it is entirely possible.
Does Dark Pit deserve to be in Smash, does Dark Pit deserve to be in Smash? He was conceived in Smash, good sir. Of course he deserves to be an aspect of the game. Whether or not he is playable, costume, or a boss-character. He "deserves" it in my subjective opinion.