Jared is/was a child actor. I wouldn't expect much of them. People are too hard on child actors, especially for a fledgling pilot. The only thing A&E could do is replace him after achieving the first season, but Adam and Eddy appear to be the types that try to hold onto actors.
Henry (1 to 6) suffers a tad bit from the pillar-style of the show (which is fairly common but it gets more noticed based on strength of writing and length of series).
Emma was the golden pillar with three silver pillars (Regina, Rumple, and Snow...who was replaced by Hook).
If you see how early on (when I felt the writing/show was more "reali" and less campy) Belle was just an extension of Rumple's story, but you couldn't tell as much of that until Season 4/5/6. You probably questioned it in 3, but you knew in 4 and beyond that she could hardly exist outside of Rumple's sphere.
The same goes for Henry.
Emma shared Henry with Regina. Regina has the villains of the episode and dragged Rumple (a pillar) into the fold. Snow was her own pillar and hosted David and Ruby, etc. It was like a 4 star solar system.
But eventually Snow and David both entered Emma's sphere and Hook did so as well, but was strong enough to be a pillar unto himself to some degree. So, Emma's sphere got crowded and that ended with Henry being "pushed out". Regina didn't "take" Henry's character, but they simply absorbed so much into Emma that Henry got the backburner when it came to Emma-Henry time.
Other than that, it's just the writers not fully realizing their story. Lying to a child for years and manipulating him is abuse, but the writers like to use deep situations but tread in shallow waters.
Also, you can tell there was conflicting beliefs in the writers' room. Lana did push for more Regina-Henry, but regardless you can tell it was more of a positive than a negative as we can see how Rumple and Belle sort of turned out to be in the end. In layman's terms, they set up something good and then to shortcuts to fix it to get to a happy ending....which happens for neaelry every plot and character arc.