First, the question of whether Young Justice incarnation of Dick Grayson is merely Tim Drake hiding under a familiar legacy name is not up for debate here.
Tim Drake does not suit the role of Robin in Young Justice. And it isn't because he's a poor, lackluster Robin. He's a fine Robin, a highly intelligent detective and strategist and skilled martial artist. And, to elaborate on a point introduced by others, Tim represents "YOU", the fan who loved Batman and managed to serve as his sidekick, tough it out during feelings of insecurity and personal loss, develop his own niche that paralleled a few of Batman's greatest attributes (detection, science, planning ahead), grow into a sidekick more serious than Dick, more sensible than Jason. Tim Drake testifies to the notion that if a person works hard, he or she can do anything set to the mind sans a motivating tragedy.
Here's where things get tricky:
How could one justify Tim's existence in Young Justice?
Tim, the ultimate Batman and Robin fan, begged his way into the role of Robin after proving without a doubt that the Dynamic Duo was Bruce Wayne and Dick Grayson? How did he do this? By observing Robin perform a quadruple somersault, a maneuver only Dick Grayson, the world's greatest child acrobat, could do. Dick Grayson plays a key role in Tim's comic book origin. Dick was Tim's idol, bot as an acrobat and as Robin, a major inspiration behind his decision to be Robin. But let's go over some possible origin stories:
1) Tim's parents are murdered, a la Dick Grayson
This origin would deepen the similarities between Tim and Bruce, two genius Gothamites from well-to-do families. But drastically changing Tim's origin is what led to the delegitimization of his New Adventures of Batman counterpart in the eyes of comic fans. Also, the murder of his parents robs Tim of the personal growth felt later in his tenure as Robin. There also the matter of ethics. If the Justice League is worried about Dick Grayson, the world's greatest child acrobat, beginning a crime fighting career at age nine, why would they approve of him training a normal boy to assist him in his endeavors? Bruce trained from the ages of fourteen to twenty-four, and STILL got trashed during his first outing. And even if Bruce forced Tim to train twice as hard as he did in the comics, the theme of Batman regaining his humanity by taking on a third protege after Jason's death would be lost.
2) Tim deduces Batman's secret identity
Tim deduced the identities of Batman and Robin after observing Robin perform a quadruple somersault only one person in the world could do. But Batman is an entirely different matter. As a classically-trained actor and all-around paranoid fellow, Bruce would be keen on separating his civilian identity from Batman as far as possible in the minds of the general public. Protecting his identity would demand using two different body languages, accents, and voice pitches. Notice that the Gotham Gazette never reports footage of Bruce Wayne swinging through the city with a grappling hook or roaming on rooftops. Tim could never figure the identity of Batman under these circumstances. And even if he did, by some stretch of the imagination, deduce Batman's identity, why would Batman take on a normally built, albeit genius boy with two living parents?
3) Tim's parents are murdered, he's taken in by Bruce, and later deduces his identity as Batman.
How would this make his origin majorly different from the journey Dick traversed to fight alongside Batman as Robin?
Lend me your thoughts, please.