I don't NIN - at all. However, I do MNK from time to time.

That said, I think the "MNKs are rocket science" perception may come from the fact that if the MNK looses GL3, they go from the (arguably) front of the bus to the back in a heartbeat, and it takes a while to get it back up to speed if you don't have PB on tap. As such, it often requires a good deal of creativity and intimate knowledge of the fight and its mechanics to ensure this stays up and running. This includes when to go ahead and pop PB for your damage boost and when to hold it back a while longer because you're going to need it again to rebuild your stacks.

As far as I am aware, and please correct me if I'm wrong - failing a Jutsu is in no way as damaging to your DPS as loosing GL. Even though you're probably greatly more likely to screw up a Jutsu than you are to lose GL.

That, and for some reason, people seem to have the hardest time in the universe remembering positional attacks. No idea why. It's only one of two positions and it's not like they ever change.

I will not say one is inherently harder than the other because I have no working knowledge of NIN - and I don't necessarily like to jump to too many sweeping conclusions based on theory alone. However, on paper, NIN looks harder to work than MNK due to a lot of snap decisions on the Mudra side that need to be made.