I'm far from a "master" (Cyber's no dmg run on MN in Black is a bit beyond my capacity), but I am rather competent in NG 1 and 2. I was much less so in NG3 on Hard. My assumption is that it either has to do with the limited options, or simply the fact that I lack the drive to improve in it because I don't care. I had an easier time going through Master Ninja in Black and Sigma 2 than Hard in NG3. I'd still say I had a tougher time in vanilla NGII's MN mode than NG3's hard, though (largely due to my refusal to use any items through 80 or so % of the game, and my dedication to trying to beat the Tests of Valor with similar item use practices).
For me, it's two reasons:
1) The limited options due to the heavily butchered gameplay mechanics. The biggest offender of them all being the removal of Dodge Canceling in favor of the lesser reflex-reliant Shuriken Cancel. I'm much more content with stopping my combos midway by dodging like I used to as I played through NG1 and NG2/S2 ( regrettably missed out on Black and Sigma 1

). The need for Shuriken Canceling just makes moving around worse if anything.
2) The health of the enemies. Just, WTH man!? Sometimes I end up OHKOing my targets with little effort, and other times I'm like whaling 20 hits on them just to get them bleeding for an Obliteration Technique finisher. It's as if killing off my targets is based on random chance, leaving PURE LUCK on whether or not the schmo dies within the current hit or the next. That, and a few moves with a high chance of killing specific types of targets that would usually take a freaking generation to beat (Example for Alchemist: *running*YYXY-Izuna-). It does not help a single bit there are 50-something opponents at one wave every ten steps you take through a stage. Even the older iterations were more lenient about this. In Vanilla NG3, it's just repetitive, annoying, and a huge test of patience. I'm a very patient person, but there came a point where I actually said "Screw this, I'm gonna go play my Jak and Daxter HD Collection and drop this trash." I'm not sure how waves come and go in Razor's Edge, but I'm hoping it's not as annoying as this >_<;
OH YES, I ALMOST FORGOT!
3) The counter system is ridiculously useless in this game. Sweet Jee Wizz....