Points to consider from tradition (D&D tradition):
Assassins have a "Death Attack" and dabble in magic. One could say, the archetype the D&D Assassin covers, is the stealthy killer that uses magic to boost its skills.
Ninjas have various Supernatural powers. One could say a Ninja is a stealthy guy that uses Ki to for superhuman feats.
Both opposed to the Rogue, who currently seems to be a shady McGuyver type.
Whether you think thats enough of a distinction to make an own class is your call.
Personally, I think the Mage/Thief killer type is distinct enough to warrant a class. Its narrow, but not narrower than the Druid or Paladin. I wouldn't mind if its included in D&D Next.
The Ninja on the other side is to specific for my tastes as a class. Some (line of) Feats would be better, like "Ki User: Acrobatic", "Ki User: Body" and "Ki User: Mind" or so.
Sorry if I'm harping on semantics, but very few things are necessary for a fantasy PnP system. One could argue that something qualifies for the genre some kind of magic user has to be available, likewise some kind of warrior. The Wizard and Fighter classes would satisfy this.
What is represented by a class, or by a feat (or whatever) or at all, is largely contingent. The reasons for including one thing or the other can vary. For Next tradition likely plays a big role, as well as player expectations and considerings what makes for an interesting game.