I think, s/lash, that my answer to your rhetorical question would be that in this instance, it would severly ruin the premise of the setting if all the players were allowed to be the "chosen ones." Same as in Buffy the Vampire Slayer, a party full of slayers would ruin the basic premise of the series, and all you are left with is a rather bland setting.
What gives the Matrix concept an edge is that the heroes are VASTLY outclassed by the agents, and must use every sly trick in the book to succeed at their goals. It's a cyber version of Call of Cthulhu, only a little more hopeful than that.
However, there should absolutely be rules for the play of a chosen, because the ability to play one should not be removed out of the game completely. But play revolving around a chosen and his core group of friends and associates requires a higher involvement in the role-assumption side of RPG's, because part of what makes the setting special is the assumption that one player will have more physical power than another. It doesn't mean that they aren't effective, just not as combat effective. It's a fine line to walk, but to remain relatively faithful to the setting, only one character (PC or NPC) should have the power of "The One."
