This is the only version I've played, so I can't really compare them. The DS version is supposedly almost identical to the PSP version, while the 3DS version is supposedly somewhere between the console version and the PSP/DS version.
The PSP version has terrible loading times, though I would assume that's not much of a problem for the DS. I've heard the cut-scenes (movies) in the DS version are horrible, but they are ok in the PSP version. The DS may also have certain control issues in regards to using the teleportation rings or cutting certain shapes in the red Lego walls.
I chose the PSP version primarily on the assumption that it would have better graphics. --- Solei: "Adell, since you're a tough guy, you don't do anything cowardly like saving, right?"