This is not a "3D is better than 2D" argument, but one of the benefits of 3D is that you can implement BOTH control schemes. Myst V did it, and now Broken Sword 4 is promising both point and click and direct control options. If more games pick up on that, we'd all be laughing.
Psst... Telltale! See above.
(Note: I'm sure this is possible with 2D games, too, but it would seem to be in a much more limited fashion.)