I also think it was supposed to be Baelfire, not Hook, who was then meant to be resurrected (as the name Baelfire from Wheel of Time strongly suggests). Emma and Bae were strongly paralleled with Will and Anastasia (whose name means resurrection in Russian and Greek).
Oh wow! That makes so much sense, if it was always supposed to be Baelfire that became the Dark One- died and was then resurrected by Emma. Perhaps it was only because they couldnt get MRJ back that they went with it being Hook..
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