All over the place I see people referring to the undersea creatures as "aliens", when it's never even suggested that they're not from Earth. B'sides, the idea of a more advanced sapient species from our own planet is way more interesting.
I grew up in the final years of the Cold War, and so I understand the earnest, optimistic wish of this movie (and others in the genre) for some Benevolent Space Brothers to make us all get along - if necessary, by threatening us with annihilation unless we prove that Not All Humans Are Bastards. But take a look back from the safe side of The Great Politics Mess-Up, and some serious Fridge Horror sets in: humanity's fate is now in the hands of beings beyond our reach (both physically and in technology), who still might decide to wipe us all out, at any time, for any reason. (Maybe we're killing too many tuna.) Or perhaps just "cull" us back to a more manageable, less polluting, pre-industrial level. Or demand annual tributes of children, or anything else they feel like... One thing this troper remembers very well from that era was the sense of helplessness, the faint fear always in the background that due to circumstances beyond one's control, the world might end today. The ending of "The Abyss" doesn't actually remove this Damoclean threat, it merely escalates it to the next level and takes the decision entirely out of our hands. Instead of human political and ideological rivals (whom we did, eventually, learn to get along with), we now have untouchable alien overlords. "God exists, and He's Atlantean." And if one includes the mental influence shown/implied in the novels, we might not even be allowed to think this is wrong. Water-nannies in our brains, keeping us docile and content... everyone lining up on the beaches, neat and orderly, for our divine masters' next culling...