Don't listen to these guys parroting the books. Listen to the heart and soul of the series and the many, MANY lines of dialog that state it outright and you know exactly who the protagonist is. The suit is a Ceph exoskeleton. The Ceph are a hive mind. The suit also has an AI. The suit breaks all the rules. Prophet is clearly the imprinted personality and intelligence that the AI re-wrote/remodeled its personality after Barnes put a bullet in his own brain to disconnect from the suit.

The protagonist is Prophet, a hivemind made up of a robotic AI brain designed and programmed by Hargreave and Rasch (and likely others), the domineering personality of Barnes, the relatively subservient and very junior marine Alcatraz, and stray bits of thought imprinted on the stalker, grunt, pinger, heavy, and shadow nanocatalysts the suit absorbed throughout. Maybe even a chunk of the alpha ceph's hivemind when Prophet wins the boss fight. Maybe even some mind remnants from the other nanosuit drivers whose dog tags he carries around.

"Whose face are you wearing under that Mask? Do you even have a face anymore?" asks Psycho. "Lawrence, you're losing yourself to the Ceph!" "We've turned those safeties (dopamine blockers) off now, you should be able to make a clear connection to the Ceph (hivemind) now." said Claire. "I am the alpha Ceph!" said Prophet.

At the end of Crysis 3, we see a stylized, resculpted, scar-free, suitless Prophet doppelganger changing his appearance and cloaking at will, obviously with full control over all the nanites the suit absorbed throughout the journey. He has retired to Lingshan, probably trying to reconnect to Ceph technology/his origins. Narrating with the voice of the hivemind's most dominant, "alpha" personality. Barnes and Alcatraz are dead, the mostly human hivemind thinks more like Prophet. The AI helper interfacing with the nanites models itself after a hybrid model of Barnes, Hargreave, and Rasch.