Eh, I probably shouldn't bump this thread with a post consisting of 'I don't have any ships of note for this one, I'm a cold fish like that', right?
Hmm...
I guess that Lacan/Sophia and him meeting the next iteration(s) of Elly would be my choice. There is very little fluff and very much of grief to be had if guidelines set by canon are to be (however loosely) observed though.
Same with Ramsus and the tangle of women he finds himself with over the course of the story. A whole lotta awkwardness and uncomfortable truths with no happy endings in sight in there. (Unless... Ramsus as a harem-shounen anime protagonist? I usually detest those, but for some reason imagining Ramsus in it cracks me up right on the spot.)
Miang/Grahf? I think 'Miang' might have tried to pull that just to motivate him in the direction she wanted - it came off as if this was the usual modus operandi for her - but I doubt it would've worked. I think if one were to write something like that, a possible starting point would be her trying to get under his skin the usual way just out of habit, repeatedly failing and the actual genuine chemistry developing over time after that.
Bart/Margie? I'll pass. It is, IMHO, either trolling or the usual
JAPAN! stuff one is better off not to think about too much. Yeah, royal lines are like that, but the narrative didn't have to bring it up repeatedly in such a manner, did it?
Fei/Elly? The only variant I think I could accept outside of just fluff for WAFF's sake would be if the current 'Fei'
did not love Elly romantically. Personally, I've found that him declaring undying love the way he did in canon felt as an asspull for me.
XXX
Not directly on the topic, but I feel that 'Miang' was supposed to look completely differently much more often than the version released as final has shown. The game being unfinished and a visual method to help the audience differentiate the characters are the likely reasons 'Miang' appears only in three different ways ('Miang - Miang', 'Miang-Karen' and 'Miang-current-Elly') - Elly suddenly changing her color scheme close to the game's end was just for us players, she didn't actually look different beyond body language, mannerisms and maybe some power manifestations (that we never see).
So, the 'Miang' Lacan came upon in Shevat's prison block was likely the second iteration of Elly he met in his lifetime - it's just she was already overtaken by 'Miang' and the 'force ghost' effect we see in the scene that made it into the game is just a way to convey that when there are no more character sprites or text panels to be had.
Similarly, 'Miang' we see in one of the slides found in the optional dungeon under the lighthouse should not look like the 'Miang' we saw either.
Hell, the name itself likely belongs to the woman whose mind 'Miang' camped out in at the time the game begins.