Both of the stories question the nature of reality, and nature of life itself. They both feature "Chosen One" messianic figures joining a group led by a bald guy, not believing what they're being told. Both have a blonde women who look strikingly alike. Both feature people trapped in bubbles.
But while The Matrix has set itself up so far as an "us vs. them" kinda battle, the beauty of The Invisibles is it went beyond the good vs. evil story. Like Marvel Boy after it, it's about looking beyond the fight, and being ready for a new age in life.
