Coming from a storyteller, I don’t feel like Neal being Bae is irrational storytelling at all. In fact, it ties into the mythology of the show perfectly. Everything else has been the product of destiny, after all. Regina adopting Henry, Regina casting the curse, Emma having Henry, Snow meeting Charming, right down to Rumple crippling himself. Yes, perhaps this means that they are referring to some higher power that is pulling the strings. Maybe it’s the Blue Fairy or the Fates! There are a thousand ways to play the destiny storyline! The greatest storytellers have used the concept of “destiny” to write the greatest stories ever written. Simply because they don’t tell you all the facts at the beginning doesn’t mean it has no “logical” explanation.
I think that you might be thinking along the lines that they’re trying to explain away the unlikely meeting of Emma and Neal a la soap opera. I can see where you’re coming from there, and if they don’t give us any more explanation of the situation, then I’ll probably jump ship with you. However, this show has a reputation for throwing the unlikely out at the beginning and slowly explaining it as it goes along.
(I would also love to address your opinion of Fantasy versus reality, but I think that’s a topic for an off-topic forum. =D)