how does one do something like this..?

[Vipershark]

That's a 3D model which has been recorded through screen capture software.

The other way to do that is through using prerendered sprites, which are essentially screenshots of 3D models.
In other words, it's not actually pixelart.

Moved to QIT.

Edit- Ah, I see. The reason it looks so sprite-like is because the color depth has been reduced to 16 colors, meaning that it naturally has a sort of pixel art look (both due to the low amount of colors and the cel shaded look that the new Pokemon games have) instead of the artifacted colors of a video but this is actually just a color-reduced recording of one of the animations from Pokemon X/Y.