They had filmed two alternative endings to this season, you can view them here…
ya i think only the one that aired though really makes any sense. If you consider the whole season.
SPOILER ALERT: (white)
And how jacob is linked to christian (who jack brought in a coffin to the island) and how locke is now in a coffin which jack must bring back to the island. Also locke is clearly heavily linked to Jacob from flashbacks from the last few episodes (i.e. when he was in hospital and when richard came to visit him as a kid).