Primarily the entry list application needs to be in at arround the 3rd of 4th last GP of they year. At that point Jenson was leading Lewis in the points and McLaren were looking at that. Lewis had a strong last 3 GP and came in ahead of Jenson who had a poor in comparison last 3 GP.
Thing is, the entry list is just that at the moment, an entry list. The final entry list should come out about 14 days before the first GP, that is more or less the final notification of who is in what car for the season ahead, or at least at the start. But by then the drivers have been out testing and that in its self more or less is confirmation.
There ane many diffrent reasons.
Look at Hispania last year, Senna decided he wanted the number 2 seat at that team last year with Chandhok being the number 1 driver. He asked and got.
Some teams go by tradition, some by driver prefrence.