If Emma was in prision, she would give her son to be adopted, Mr. Gold would bring him to Regina… and the clock goes on till Emma’s 28th birthday with all the pieces already in the chessboard. If Emma and Neal would start a live together, then Henry would grew up with them and the play never started.
I read somewhere that we will see what happens when a person from our world goes to Storybrooke. So, probably, Neal was just waiting, now, Emma is free from her duty to her people, and is free to be with him again. I guess Neal is going to appear soon in Maine looking for his beloved to find out that he has a son, and other “funny” things.
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