I've played both versions not far apart from each other, I like them both, but I think each version has its own advantages, to me the graphics on the PC engine are FAR superior in pretty much every way, more colour, more detail, better animation, you know the gist, and I also found the PCE version to be considerably easier, which I find to be a good thing considering how brutal the NES version is...
But the NES version I found to be a little more responsive in the controls and I like the music better on the NES, the PCE music isn't bad at all, but I think the instrumentation could have been better, but the compositions on the NES I found to be just that much better!
Also, about the choppy parallax scrolling on the PCE, it gets better in the later stages, in the first stage it's really jarring, but in the 3rd and 4th stages it's passable... I'd have preferred no parallax scrolling, or at least a smoother scrolling in spots, even if the backgrounds looked more repetitive...
Neither is that good. Ninja Gaiden 2 is better, lol.
Agreed, Ninja Gaiden 2 fixes a lot of the problems of the original, and because of that it's a lot better and more fun, also, it's the only game in the series I've beaten...