I mean, when you think about it, long before we knew Neal was Baelfire, Baelfire’s story was with his father. That’s how the character was originally introduced. We met him first as 14-year-old Bae. To me, that says, his main story was always going to be rebuilding his relationship with his dad.
Whatever happens with Emma, is secondary.
I think Neal will be going on a quest with Belle to figure out what happened to Rumple. That makes sense to me because they both have a vested interest in seeing him again..