If that was on an old 3DS, that was probably true. On the "New" 3DS, though, with the additional eye tracking to make sure the 3D effect is stable, it's superb.

I played through the entirety of the Metroid 2 remake with 3D on on my New 3DS, and it was dazzling. No discomfort or headaches, just a constant sensation of disbelief that this can even work without some kind of glasses on.

Does the eye tracking work with older games, or is the 3D baked into the game engines?

Yes, the eye tracking works with old games just as well as with new ones; it seems to require no software support; it just does its thing, dynamically adjusting the parallax barrier so that the left and right frames provided by the game will be seen by the correct eyes, even if those eyes are off-center, moving, or etc.

Just the way you worded this, leading me right up to the end of the comment, made me laugh pretty loud.