Here's how I see it. At this show's most basic premise, a happy ending is when you find your true love. It may also be defined by the triumph of Good over Evil. The basic story and happy ending of Snow White and Prince Charming, pre-ONCE, is when Charming awakens Snow with a kiss. The kiss also serves as a victory over the Evil Queen's curse of Snow White...so that happy ending may also be seen as a victory of good over evil.
With regard to the storybook, I think we're being led to believe that the writer of the book does have some actual power over what happens to the fates of the people being written about. I personally don't feel this absolves the storybook characters of the consequences of their actions, but I do allow for nuance and gray areas, and, more importantly, the chance for people to change for the better. I don't think the writer is a puppet master controlling every action of every character at all times, and I think Regina would agree with me. I think Regina believes that the author of the storybook (and the morals and mores of the Enchanted Forest) do not allow for bad/evil characters to be good. That once a path is laid... once a villain, always a villain no matter what positive changes one makes in his or her life, no matter what manner of restitution one makes, that person can never attain happiness. So in Regina's case, despite changing enough to earn the gift of light magic and a second (or third, since she bailed the first time with Robin) chance at a Soul Mate/True Love, she has just seen her last chance of happiness dry up before her eyes. She truly believes Robin was her last chance. In the language of the Enchanted Forest, there is no chance of love in her future. And the lesson of 'villains don't get happy endings' has always and keeps getting drummed into her (ONCE has stressed this time and time again). So the only way to change her fate is is to change the storybook; to find the author and change the ending.
I think it's pretty clear that Emma and Regina aren't exactly besties at the moment and so any magical sessions would be suspended at this time. :) What I hoped to infer earlier was that, yes, as you and others have noted, Emma has struggled with her magic and we've mostly seen her do it and succeed while under emotional duress. However, the show actually addressed this for once (yay! Also, pun!) and so we've seen Emma train with Regina and specifically seen Regina advise Emma how to focus and hone those emotions so that Emma could reliably use her magic. Emma's not there yet, but she obviously takes a lot of what Regina says to heart, so I believe Emma absorbed Regina's magic tutorials and expanded upon it during her solo (also off-screen) practice sessions in between crises and we may have just seen the fruits of her labor in Sunday's episode. Or maybe it was just another burst of over-emotional magic. But I prefer to think of this as progress. More shame me, I guess.
I think the show is way too inconsistent about magic to get too deep into this conversation (about magic, heh). However, I'm not discounting possible reasons (aside from increasing the drama) for the gold box. When I think about all of the hearts that have been taken from characters...something special has been done to those people that the writers could argue would preclude the need for a special golden box. Regina put a protection spell on her own heart before removing it. (Cora was a witch, so hers was probably protected but her box was probably platinum.) Henry's heart is protected too. Aurora and Snow survived sleeping curses and were revived with TLK, so maybe their hearts are somehow inured to whatever storage container befalls them. Marian is just a regular heretofore healthy uncursed person who was/is now suffering under a freezing curse. Maybe the gold box stabilizes the heart in some way? I don't know. I gave up on rationalizing the magic stuff when the show did in the Season 2 (or was it the Season 1 fairybacks?).