Ninja Gaiden PCE is just using dynamic (animated) tiles incorrectly to create parallax. Many PCE games use dynamic tiles perfectly for parallax and the PCE can do much more than 2 layer scrolling. Metamor Jupitor has a stage with 4 layers of fully overlapping scrolling, of which one layer is a transparency effect which fades in and out over the 3 layers behind it.
I find the PCE version less frustrating than the NES version. If I remember correctly, in the PCE version, your sword actually damages enemies. In the NES version, enemies can only be damaged by the space directly in front of your extended sword and if an enemy is close enough to touch any pixels of your sword, they take no damage and instead your are hurt.
I also prefer the NES soundtrack. Many NES games sound as good as or better than 16-bit version. Ys III for example.