I tend to envision XMFC as a reboot rather than a prequel, because the very thought of X3 still makes me cringe, but I'm glad you're of a different mind, since it produced this story.

Lucid characterisations (of Raven and Erik, though my favourite part may have been Charles's anger), and a convincing take on the dying days of a terrorist group, confronted with the reality that the world is a more complex system that they can ever dream of in their unilateral philosophy.