Thing is, Kojima wrote himself into a corner with the Patriots. He kept them so mysterious and bizarre that all sorts of theories were floating around about them, some so far going as to say that they were the original ghosts of the founding fathers of the US. Yet the truth was so mundane that a lot of folks felt it was a major letdown when the revelation was they were just AIs
who manipulated the media and stock market.
Just like I said in the post above: it all comes down to the need of an editor. Kojima honestly could've accomplished the same 4th wall breaking effect with them without resorting to making them into some incomprensible gibberish speaking-AIs
For example, instead of Rose being a real person, he wrote that the ROSE AI was still desperately trying to convince Raiden that she was real until the very end, and made it that Rose never existed - only the "memories" of her that Raiden had. The fight with Solidus would mostly stay the same, but instead he would be lecturing and tormenting Raiden with the fact that everything about him is fabricated, meant to be a copy of Snake and a test of his willingness to play along, nothing more. It would've still tied into the theme of Raiden's world being what players would want their own character's (or their own life) to be like, yet being artificial. After Solidus' death, the rest of it all would stay the same, except for the change to Rose and the Patriot's identity. No need for the AI Colonel - you can remove him from the plot around the time Arsenal Gear crashed into Manhattan. You can speculate that his AI was destroyed by the virus.
Then again... such a change would actually be pretty significant. Making Solidus aware of the true plot would mean that the Patriots aren't some type of invincible, untouchable force which cannot be understood. The idea that absolutely NOBODY
, not even Ocelot, knew what the hell they were was critical, since it forced the player to accept the fact that fighting against them is futile: you can only try to co-exist or ignore them (both at your own peril).
Would you believe I never fully watched the original Indiana Jones trilogy? I gotta correct that someday.