Taking into consideration what bungie already changed about the canon, they could've done just a little more to make master chief more involved and strengthened his connection to the game.
First off, it is completely uncharacteristic for Master Chief to be sleeping while the battle for reach is still going on. The whole him sleeping while soldiers are outside dying is so unlike him. He is the LAST person to give up before a battle is over.
So why not have master chief still awake and fighting when noble 6 and emile get to the pillar of autumn? He and linda could be posted up outside the autumn. The idea being that operation red flag was abandoned now that reach is going to fall, so all remaining spartans are to return to the pillar of autumn to prepare to embark on a new mission in lieu of dr Halseys new discovery, which they are told is being delivered by noble team. Of course, Chief and Linda are the only two that make it as all the other spartans are thought to be dead, or unable to get there.
Master chief doesn't even have to recognize who noble team is, in light of the situation where the whole planet is being burned to the ground he'd be plenty thankful that they made it with the package.
So emile and six make it to the autumn and meet up with chief and Linda. Keyes informs them that they need to clear the landing zone so they can pick up the package and get them out of there. The four spartans defend the landing zone against waves of covenant. In the firefight Linda gets severely injured (like she did on gamma station). Keyes comes to pick up the package and the remaining spartans but emile dies in the mac cannon. Chief carries lindas body on board the pelican as this happens. He turns back and being the duty bound hero he is, he offers to man the ma cannon so the poa can escape. But noble six says something along the lines of "No, she chose you for a reason" (referring to cortana), "I have the gun." And instead of keyes we have chief saying the line "good luck spartan." Which is a reference to the fact that Chief has amazing luck.
We would also have to change one of Dr. Halseys lines when she is giving the package to six. Instead of saying "there you will find a halcyon class cruiser waiting to get her off planet", it would need to be something more like "Spartan-117 and his men will be meeting you there to get her off planet". Otherwise how would he know cortana "belonged" to the chief?
I feel a change like that would bring things together so much better. Chief sleeping is flat out silly imo.
[Edited on 01.20.2011 7:13 AM PST]