Besides putting the main storyline on hold for nearly a decade to do a flashback story, it's been said that Kojima REALLY REALLY REALLY disliked fans in the west that disliked the made by committee to appeal to lowest common denominator female fans character Raiden. So to punish the western fans, Kojima essentially decided that Snake's face and body would now be used exclusively for young Big Boss. Which is why Snake was a gray haired old man with a mustache in MGS4 and why Konami has to overrule and tard wrangle to the extreme Kojima during the lead up to the game's release. Kojima wanted to explicitly go full mystery box the fans ala MGS2 and pull a bait and switch, making them think they were getting a new game with Snake as the lead character but not knowing until the day the game hit shelves and people bought it, that it wasn't a continuation of MGS2's plots but a flashback story and you play as Big Boss not Snake. To the point that the first round of screen shots sent to game magazines were vague as fuck and didn't state the lead character was Big Boss.
Konami put a stop to this ASAP and went public with the plot and identity of the main character, then demanded Snake be the lead in MGS4 as a non negotiable "you will do this or be fired" edict from high, which led to Kojima making him old as fuck as a fuck you.