Supergeek time. Ready? (Apologies if this has already been covered in a previous post.) I say Neo might not be dead. There is a visual cue that could point to this.
Something occurred to me while seeing Revolutions. When Neo is blinded by Bane-possessed-by-Smith, Neo's "vision" of the world around him becomes a sort of glowing golden effect (contrasting his drizzling green-code effect of "sight" while in the Matrix). It's what lets him "see" Smith through the burns and fight against Smith/Bane. Later, when Neo is walking through the tunnel toward the area in which he meets the Babyface Machine God, he also sees things glowing golden, if I remember it correctly. Later, Neo is beaten by Smith in the Matrix - and he also "dies" in the World of the Real - and his body is respectingly taken by the machines... But... We see this happening in glowing golden effect again, this time from outside Neo's body. So if we've only seen this glowing effect from Neo's "vision" / Neo's body's point of view, then who's point of view are we seeing his body being taken away through?
Is Neo really dead, or is his consciousness just now one-with-the-machines, digitally godlike and mechanically omniscient, like The Major in the Ghost in the Shell films? Tough to tell. (The movie ends so abruptly that the Wachowskis might not have given it a second thought.) Maybe I'm reading too much into it, but it does stick out in terms of visual narrative choice.
(I haven't played that ancillary Matrix Online MMORPG, but I heard that even though it takes place after Revolutions, the legend of Neo and his influence still figured into the narrative.)
Just a thought. :)