JC is a metaphorical acronym for Jesus Christ - JC Denton in the game is a transcendental figure whose character progression inevitably results in creating the "new man" - he's defining the transhuman reality. Thus the box art where Denton, bathed in light, looks up at the sky (heaven).
Page wanted to dominate Helios - Helios viewed himself as indispensable to the future and thus couldn't merge with Page. The most heart to heart conversation in the game was between Morpheus (who later rose like the sun to become Helios) and Denton, and it was clear that Morpheus admired Denton.
JC is not himself after the merging - this merging parallels that at the end of Ghost in the Shell - it's understood that the only moral merging is both entities losing themselves to create something new. Both Helios and Denton are lost and something new is created.
All of the main characters in the game are attempting to be this messiah - Tracer Tong, the Illuminati, Bob Page, Helios. Helios recognizes his limitations as a computer program and is expanding the capabilities of his program by merging with Denton, thus enabling the best possible transhuman reality in his view.
All of the messiah figures, including Denton himself, are dark and sinister (the game takes place entirely at night), and the oppressed enemy in the game is not so much the various messiahs opposed to each other, but regular people, who are killed off and/or weakened by the plague.
Deus Ex depicts a world where regular decent people suffer terribly and die while the power elite fight among each other for global domination.
Helios is the technocratic option, corresponding to the computerized security/surveillance state illustrated clearly by the recent Snowden revelations. The Echelon system in Deus Ex has similarities to the NSA system.
Page and the Illuminati are two types of dictatorships - the iron fist versus the velvet glove.
Tracer Tong is the ironic luddite - using technology to destroy it.
JC Denton, despite being well meaning and declared by the game itself to be a savior, cannot produce a good outcome. He can only choose the lesser evil.
The good possible future, that is to say democracy, is made impossible by a combination of the plague and the global police state. Instead of fighting the powers that be, the people reach out to the same powers that caused the plague to grant them the cure, cynically named Ambrosia, "food of the gods" but actually merely a life-extender for ravaged and dominated humans barely continuing to breathe.
The "aliens" in the game correspond to the "evolved man", ala Olaf Stapledon's "second men", yet keeping with the dark irony of the game are actually just genetic cross-breeds.
Inspirations for Deus Ex include Ghost in the Shell, Metal Gear Solid, System Shock 1 and 2, the Matrix, Neuromancer, and the works of G.K. Chesterton.
Although Deus Ex is the best computer game ever made, it's fundamentally flawed in it's optimism - the powers that be in the real world aren't interested in creating the "second men", but rather simply maximizing their wealth and well-being in a dying world. Deus Ex believes in a radical shift in the nature of life (from human to transhuman) whereas what's at stake in the real world is the existence of life itself.
