The aliens aren't exactly characters—but then, other than Hal, there aren't very many convincing characters in the book anyway. David Bowman, Moon-Watcher, and Heywood Floyd all stand in for "humanity" more or less. By the same token, the aliens stand in for "God", or "evolution"—or, possibly, for Arthur C. Clarke himself. The novel says, "in all the galaxy, they [the aliens] had found nothing more precious than Mind" (37.5)—which tells you pretty clearly what the book sees as important. The aliens cultivate mind; they make the brains that go from earth to the moon to space.
Those brains are mostly indistinguishable, whether they belong to Moon-Watcher or Bowman. The aliens want minds, not hearts or souls. As disconnected intelligences, without bodies or personalities, they seem to sum up the kind of characterization the book sees as ideal. They are the non-characters who sum up the non-characterization that characterizes the book. The aliens are nobody, and, the book seems to say, if humans evolve just right, all of them will be nobody too. Um…yay?