Just finished watching this thing. Many opinions follow...
This film was the Anti-Matrix. 4D STS propaganda for itself.
The word "God" was never said directly, but we are led to believe that the men in black were angels. (Had been called that, anyway), and that the all powerful being in charge, the mysterious, "Chairman" is a kindly person who would just LOVE to give us our own free will, but shucks-darn, every time this is attempted, we silly humans screw it all up by starting wars and dark ages, etc.
So he just *has* to step in with his legion of reality-morphing bureaucrats, and when they fail, 4D truncheon-wielding shock-troopers in black, (yes, really; God apparently needs riot police.

), to maintain order among the stupid people. It's all our own fault for creating this mess, you see.
Never is it suggested that the whole thing might in fact be reversed; that the MIBs are responsible for hell on Earth. That slight deviation from truth was the most aggravating; I think it's safe to say that we've all experienced the Matrix trying to mess up our plans. When I was a kid, before I'd been exposed to any esoteric writings at all, I noticed this force and dubbed it, "The Dark Gods", and I fought on through their bullying schemes with gritted teeth. I joked about it at the time, of course, (though deep inside I felt there was some truth to it all), and was not terribly surprised to discover that my "Dark Gods" were indeed far less a fantasy than I knew at the time.
This film names that force, puts a face on it, and then calls it "love".
What a load of BS!
The more I think of it, the more I wonder how the heck a film like the Matrix ever managed to get made! Maybe the PTB saw all the kung-fu, explosions and black leather, and then rubber stamped it on that basis without reading the liner notes. Evil is stupid.