Donning my dorky 3D glasses and engaging in a few Arcade challenges with Ska Studios marketing coordinator, Dustin Burg, I saw first-hand how 3D changed the game -- not just that things appear to leap out of the screen, but that the smooth, 60 frames-per-second gameplay of the standard game is halved when turning on 3D.
As for the genesis of 3D mode, it actually started as a modifier in the game, where a power-up would turn on a red-and-blue visual filter. "Our producer saw that and said, 'Dude, you should just put 3D in the game,' so James bought a 3D TV and started to play around with it." Burg also explained that the exact effect of the 3D would change depending on the level you're playing, so it wouldn't always be 2D art layered for a 3D effect.
On paper, it seems like a dicey compromise, but in motion it's not a bad trade off. While the dip in frame rate is noticeable, it doesn't ruin the experience and bolsters an already stylish game. 3D enthusiasts could easily play the game with the added visual flair and have an experience comparable to non-3D users.