Hmm. For me, INS has generally been one of the better thought out plots in Star Trek. It confuses a lot of people because nothing is what it seems at first.
First, there are disguises and camouflages - invisible invaders walking among the unsuspecting. Then, there are hidden truths about the nature and identity of the victims, some revealed at this stage, some not. Then, further disguises and camouflages - invisible ships under water. Then, major revelations about the nature and identity of the villains. The proper response of a hero to the events depends on what he knows; what's proper in Act 1 turns out to have been dead wrong in Act 3 and so forth. Everybody is being played for sucker right down to the second-to-last act where the villains finally get a taste of their own medicine.
"Layers" is different from "depth", but it tends to be more interesting, and perhaps more lasting.
Not to say that a TNG movie couldn't have done a "layered" plot on the Dominion War, of course. But no good war movie ever featured a clever plot that dictates the outcome of the war - that's downright cartoony. Good war movies may instead use wars as backdrops for clever plots that dictate major turns in the lives of the interesting characters, after which the war either goes on or ends all on its own.