It just depends so much on what Hook and Rumple do from here on out. Right now, they’re on somewhat equal standing–they both helped put Storybrooke and Henry in danger in various ways, they both betrayed Bae (at least from Bae’s POV) a long time in the past, and they’re both only narrowly-reformed villains who seem to slide back and forth over the good/evil line like Lacey walking home from the Rabbit Hole at 6 am. Nobody’s ever entirely sure whose side they’re on at any given moment, and Regina and the Charmings know it.
Regina, though she’s usually the hothead of the three “villains” on board the ship, may actually be the most reliable of them as long as Henry’s in danger, because the one motivation everyone can count on with her is protecting Henry. Emma knows it at this point–she’s seen what Regina’s willing to go through for Henry’s sake–and so she’ll trust Regina that far. It’s likely she’ll trust her even further than that because initially Hook was like “I’ll take the bean and escape alone” and Gold was like “Eh, we’re all gonna die, what’s it matter now?” when Storybrooke was threatened, while Regina actually planned to sacrifice her life to let them escape–if only for Henry’s sake. She’s done more to redeem herself but (from my perspective anyway) had a lot more to redeem than the other two (who have killed and harmed others, but far less gratuitously that we’ve seen).
I’m rambling again. But I totally agree there’s a strong parallel between the Hook-Rumple connection through Bae and the Emma-Regina connection with Henry. I hope we see that played up. Their little truce makes sense–they need each other to save Henry, Hook’s been rethinking the whole revenge thing since he realized he hadn’t succeeded, and Gold knows full well that Belle wouldn’t want him to kill Hook if only for his own sake. She has the interesting effect of both sparking his violent outbursts and quelling them.
I do wonder how the ladies and David will play into the relationship between Hook and Rumple at this point. David, especially, since he and Emma are pretty much the only people that Rumple actually has permitted to see his more vulnerable side besides Belle and Bae. He trusts and admires the two of them more than he does most people, even if he mocks David Nolan a bit–David’s the one person he trusts to understand about Belle, and we know that part of him kinda wishes he could be Charming, but David’s also the guy who locked him up in FTL (whether he wanted it or not). And David’s not especially fond of Hook–see their rather violent altercations every time they meet–so who knows what kind of relationship they’ll forge. Yet they did manage to work together when they were playing cops.
Emma’s relationship between the two could be even more complicated. She’s declared LOVE for Rumple’s son, and bore his grandson, and she’s acknowledged him as family. Yet there’s clearly some attraction between her and Hook–either romantic or kindred spirits or both. I think she’d fling herself between the two of them in an instant to stop one killing the other (we’ve already seen her do this a couple times, actually, in 212 and 215). And we know that Hook appreciates much about Emma, as does Rumple.
Regina and Snow seem kind of on the outside of this dynamic, but they might wind up being drawn in at some point. OMG, is it autumn yet?
Keeper of Belle's Gold magic, sand dollar, cloaks, purple FTL outfit, spell scroll, library key, copy of Romeo and Juliet, and cry-muffling pillow, Rumple's doll, overcoat, and strength, and The Timeline. My spreadsheet: https://drive.google.com/file/d/0B6r8CySCCWd9R0RUNm4xR3RhMEU/view?usp=sharing