Well, my 'embryonic' GF V storyline, includes a flashback to the early 1970s... maybe 5 years before the beginning of GF III. (And also the pre-pre-prequel sequence, in Sicily in the 1890s, and the final epilogue in 2001-2004.)
In my GF IV plotline, I have Santino Jr., estranged from Michael and the rest of the family by decision of his mother, Sandra, who was resolved that Santino would grow up 'legit', turning to the outlaw way of life after a mid-life legal and financial disaster leaves him ruined economically and deserted by his wife and family.
At the urging of Kay, Anthony makes a 180-degree turn, rejects opera singing, goes back to law school, and wants in to his father's business. Kay and Anthony are utterly obsessed with one goal - making those guilty of the death of Mary, pay with their lives. (Of course, this might ultimately include Michael or Vincent.)
Anyway, to resolve the Tom Hagen situation, I would work in one of three 'flashback' sequences in GF V.
At this point, 1972-73, Tom Hagen would be sick with cancer. (This would allow the appearance of Duvall, who is now in his late 60s, in the movie, simply explaining that the cancer treatments have him looking drawn and aged.)
Hagen would be involved in legal maneuvers to start to take the Corleone Corp. legitimate, and also legal maneuvers to keep Victor and Michael Francis Corleone out of prison - both of them, in my opinion, would be heavy into crime by this time, since as young kids in 1959 in GF II, Michael said they had 'already been picked up for shoplifting.' By the 1970s, they'd be heavy into drugs and crime.
I'd have Victor getting killed in a drug deal gone wrong, and Michael Francis gettting sentenced to a long prison term. (This explains where he was during GF III.)
Tom Hagen would begin maneuvering to put pressure on Pat Geary - by now, Vice President of the United States - to deliver a presidential pardon for Michael Francis. But this bid fails - it isn't until 10 years later, 1982-83, that it succeeds and Mikey gets out.
By this time, Hagen's loyalty is no longer in question - we find out through dialogue that he left the Corleone Family in the early 60s, and after a hit attempt gone wrong, helped deliver the Corleones a rival boss for a hit of their own, redeeming himself in Michael's eyes and returning as Michael's second-in-command.
But like Genco, he dies of natural causes, just before a time of great tribulation for his Don.
Just as Vito was left with a weak consiglire, so is Michael. Tom Hagen was weak in the 1940s simply because of youth; later as he got older and wiser, he became every bit Genco's equal. But Michael Corleone is stuck, after Tom Hagen's death, with B.J. Harrison, who is just an airhead pretty-boy. In a way, Harrison is like a mini-Fredo - he's just too stupid to entrust with anything important.
In the events of GF III, Connie of course becomes, for all intents and purposes, the consigliere.
