Aera and Lynn in Swordcraft Story 2.

Pandora's Tower has multiple endings like that, with Ending B fitting your description best. Just get Elena's affinity up to 5 or 6, and make sure you emulate it, because the last dungeon is bugged to crash often on real hardware. Sin and Punishment 2 has a twist ending almost like that if you beat the game on Isa and Kachi mode, but it's such a sudden cliffhanger, you don't even see it register with Isa.

Valkyrie Profile, while Lucian and Lenneth's story gets resolved in the true ending, the Einherjar aren't reunited with their partners.

Majin tensei has it as a big vocal point with the main relationship. There is a true ending where there is no death, but there is 20+ things you have to do in game to get it that it's pure bullshit the amount of times you have to replay a single 2 hour stage for a different cutscene to explain one thing in the sequel. Unless putting in 8-10 hours worth of grinding for the true ending, the normal ending is good enough.

I vaguely remember this guy back when I played FF4 https://finalfantasy.fandom.com/wiki/Edward_Chris_von_Muir >Edward Chris von Muir >Edward was born and raised in Damcyan, but disliked the idea of playing politics and preferred music. He traveled the land as a bard and fell in love with a girl named Anna. When Tellah, Anna's father, did not approve of their union, the two ran away making Tellah furious, and he followed them looking to take Anna back. >(...) Anna dies. Having lost his parents, his love, and with his kingdom in ruins, Edward breaks down in tears. Cecil slaps him across the face and demands his help, (...)