A flatter perspective definitely throw off the PCE version. But it is more than just the perspective, there is a wonderful organic, grittiness to the NES version that is completely lost in the sterile PCE version.
I feel that one of the primary reasons for this disparity is due to how jumping and slashing (arguably the most important play mechanic in the game) differs between the two versions.
For example, In the NES version I’m able to slash both of the first two lanterns in level 1 in one jump (making me feel like a ninja in the process), with the first one being hit on the way up and the second on the way down. In this version I’m almost always able to connect a rising slash, which is essential for dispatching birds, bats, umm… lanterns, and most everything really.
However, in the PCE version I find myself missing the first lonely lantern entirely about 80% of the time while performing a rising slash with the sword clearing well above it. This is even taking into account that the first lantern here appears to be set about 8 pixels higher than it is relatively set in the NES version. In fact, I can’t even begin to count how many times in a session my sword completely clears the top of my intended target (much to my dismay and frustration). I haven’t really done any research into why this is the case, but it seems as though either the jump + slash collision detection starts ever so slightly late, or the collision box is shaped differently/awkwardly from the NES version.
For this reason, and though I am able to competently complete either game, I actually find both versions to be roughly equal in difficulty (albeit for completely different reasons). The NES version just makes me feel more like a ninja doing so.
