Recommendation: Your brain actually has two depth perception systems: hardware (using your two eyes for parallax) and software (using visual cues to establish a 3D scene, the way you can with one eye, or when looking at 3d projections onto a 2d surface).
Use each depth perception mechanism for a different axis! In this old applet you could enable stereo projection and also thick-lines-mode which really helped this, and gave me a strong intuitive feeling for the motions of the hypercube.
Recommendation: Your brain actually has two depth perception systems: hardware (using your two eyes for parallax) and software (using visual cues to establish a 3D scene, the way you can with one eye, or when looking at 3d projections onto a 2d surface).
Use each depth perception mechanism for a different axis! In this old applet you could enable stereo projection and also thick-lines-mode which really helped this, and gave me a strong intuitive feeling for the motions of the hypercube.