Grogan > Eason is an easy call, at any point, but Montana > Young at that particular point in time I'm not sure I buy. That Cowboys team was younger, bigger, faster, stronger, and hungrier than that Niners bunch and Young being the vastly more mobile and pliable of the two I think helped keep them in that game. SF went 14-2 and got HFA with Young all the way, so I think the Morrall '68 comparison is a little more relevant because Unitas barely played that year - it would have taken extraordinary balls to go away from what had worked so well all year (same spot Seifert was in), against a team you considered yourselves better than anyway. The Dolphins team was a lot more run-heavy than the '68 Colts so I think Griese/Morrall were interchangeable parts on that squad, though of course that's easy to say because they won. If only they'd remind us once in a while....
As I'm a "let Brady play until he sucks" guy this will sound counter-intuitive but the Niners also could have wrecked their future because they got 6 more great years out of Young (and a SB) after that game. Joe was still very good in KC - it's hard to say what his stats would have looked like in SF instead of playing MartyBall in KC - but he had pretty clearly deteriorated significantly physically by the end of those seasons. To bring it back to Brady, I think the point at which using Montana/Young as a corollary to TB/JG fails miserably is that Tom hasn't shown any signs of deterioration or had any repetitive injury issues (knocks wood), and JG hasn't started most of two full seasons and posted 100+ passer ratings. If either of those things were remotely true at this point I may feel differently about the situation, I'm sure there were many Niners fans who would rather they let Joe play it out if it meant maybe he'd get a shot at one last SB ring...even if that means some day you have to watch Tim Rattay start. There was just a lot more verifiable evidence that Steve Young was for real (and that Joe's clock was ticking loudly) by that time than the highly circumstantial reviews some are giving JG based on "how his poise looks", or whatever.
Personally I think Haley & Co. would probably end up knocking Joe out anyway, that game was very physical to my recollection, and while I doubt Joe would lack confidence in that scenario I don't think the one half of football in 2 years against a pretty bad Lions team would be enough to make me bench the MVP. But I suppose there's an argument to be made that the surprise value of a Montana start (or coming out in the 2nd half) could swing what was a very competitive game that was basically decided by 49er turnovers. So fair enough, it is your opinion, and it's certainly an interesting alternate history to think about.