Step 0 is missing: having a great taste. One look at the video example is enough to figure out that the author keeps things in balance and in style. Explanations of why pixel grid mismatch looks wrong, or why mismatch between texture density and geometric complexity (in both ways) looks horrible, or why smoothing does not blend with pixel art are then made in retrospect.

Some details are a bit too cool for 1993, though, and assume high frame rate (won't work that well at low fps). Smooth weapon animations with a lot of frames, tiny per-pixel effects on bullet holes and flash sprites, smooth movement and object position calculations that use precise math instead of fast rough estimates resemble Chasm: The Rift or Quake (the concept of idle animations, e. g. objects moving in the starting view of difficulty selection room, assumes that there is some performance to waste on details that make the world less empty).