It is an innovative thing and it's part of FFXI uniqueness, but that doesn't mean the game can't be better without it.
Surely THF (and a lot of class) without /NIN will suck, but that's because it's overpowered. They should balance the basic of the classes instead.
SE just don't have the guts to fix that hole and instead let more and more people to be dependent on it.
It could have been the number of shadows used is dependent on the actual damage absorbed, that way people can still use the spell for protection, but PLD (comeon, it's a /NIN, not a NIN) won't be mitigating 90% of physical damage of most HNM.
The entire art of keeping shadows up and keeping max haste on PLD might require some skill, but once you get used to it, every fight is the same. PLD build hate, BRD RDM keep hasting, WHM keep spamming cure.
The spell might be innovative but it's limiting creativity at the end, because anything else is so less efficient and unsafe that no LS will do them.
What you are basically asking for is for SE to nerf the optimal build. If they do this people would just find another optimal build and do that instead. You are not going to get people do use a variety of different ways to accomplish a task. They will find whatever is most efficient and stick with it. It is human nature to do this.
What you are asking for is impossible. It is the nature of MMOs (and in fact nearly everything) that there will always be an optimal way of accomplishing a thing. It is impossible to perfectly balance everything. The only thing you can do to prevent it is keep nerfing the optimal build and if they keep doing that eventually people will just get pissed off and quit the game.