The NES version is still my favorite one.
I have tried to get into the PCE version, but it hasn't "clicked" yet.
For all the flaws of the NES version (and believe me, we knew the game had flaws back when it was released), it is still the vastly more enjoyable experience. Yeah, I am masochistic...in that I enjoy many games that have moments with harsh platforming.
In Ninja Gaiden NES, you can ABSOLUTELY pass 99% of the challenges with basic platforming skills.
There are, however, several spots in NES version where you NEED A POWERUP in order to advance *safely*. This is not a flaw. It is perfectly acceptable, albeit more challenging, to require an item to progress unscathed. if you think this is "cheap", then it means that only a few moments in the game are "cheap", IMHO.
I am certainly going to give Ninja Gaiden PCE another chance to win my love, since it has been a few years since I have played it...