Id like to see a sequel with him as the main badguy. But as a developing/fluid plot twist. Continue on shortly after RDR and as the game moves along he starts to turn his focus and ends up being the villian.
Okay, I know I said I thought this was a bad idea, but I've been considering it, and I think I might have come up with a way for it to work. It's a bit long, but I think it would work:
The story would have to re-tell "Remember My Family". Agent Fordham is inexplicably absent from the final cut-scene of "The Last Enemey That Shall Be Destroyed". A sequel would explain this absence as Fordham's disgust at Agent Ross going back on his deal with Marston, whom Fordham believed had redeemed himself. Fordham requested a transfer and left West Elizabeth, but Ross realised that he had taken the original files on the deal with John Marston with him, and arranged for Fordham's death. Fordham saw it coming, and bequeathed a letter to Jack Marston as part of his will. The letter explained what had happened, and included all of the files. It told Jack to seek out Agent Ross; what he chose to do then was up to him, but he had to give Ross a letter of his own first. Jack follows this instruction, and Fordham's letter to Ross explains that Fordham felt that what Ross did to John Marston was wrong, but rather than go through a lengthy trial, he thought the best thing to do was to tell Jack everything and let him decide what Ross's fate should be. One Ross finishes the letter, he asks Jack what he wants to do, and the two duel.
The story then jumps forward to a new character, a US Marshal who was disgraced and sent out to the province beyond New Austin. This character is given the chance to resume his former position if he investigates the death of Agent Ross. The player begins chasing after Jack Marston, believing him to be a villain. At the end of the second act, the truth comes out: Nate Johns, the state governor during the events of
Red Dead Redemption, conceived the plan to use John Marston to bring in his former gang, credit it to the FBI, and use this to stay in power as governor. When he started losing support, he and Ross conspired to kill John Marston and present it as the FBI bringing in one of the country's most-wanted outlaws. Johns was re-elected and Ross became one of the FBI's most-decorated agents. Now, three years later, Johns is seriously considering a bid for the presidency at the next election, but realises the implications of Ross's death and tries to have the player character kill Jack Marston to cover up what happened. The third and final act starts with the player character and Jack going after Nate Johns.