I came up with a few more.
Final Fantasy:
Bartz / Farris
(also: Firion / Leila)
bartzxfaris2.jpg
I don't buy the Lena / Bartz romance at all, but this is a pair I always have. The idea of two free spirited, adventurous people exploring the world together, with a strong bond of friendship and hardship shared between them growing into something more just works too well for me not to ship this couple.
A similar situation occurs with Firion and Leila in FF2, although the intention to pawn Firion off on Maria is far more clear in that title (which is unfortunate considering how much of a shell she is -- I swear she just exists to follow Firion around and provide two sentences of drama with her brother). Leila isn't the best defined either, but I get an innocent feel out of Firion and see the more worldly, driven pirate lady working better for him than the empty tag along.
SaGa Frontier:
Asellus / White Rose
Saga.Frontier.full.126771.jpg
Though the game never outright, to my recollection, says or implies this relationship is romantic, I'm fairly certain everyone that played through Asellus' story came to the conclusion it was. Their bond is quickly established by the game and I always felt they were growing closer as Orlouge continued attempting to recapture them. You also cannot ever recruit one without the other.
Tales of Eternia:
Farah / Rassius
images.jpg
This is one of those pairings that the game goes out of its way to prevent being a thing, as Ras and the Princess are clearly attracted to each other and Farah kind of has Reid going for her, but this was always the pair I wanted instead. Reid / Farah work much better as childhood friends and Farah ultimately reshapes Ras' path in life -- it could have been a really great romance if Namco had decided to pursue it.
Lunar: Eternal Blue
Jean / Hiro
JeanHiro.jpg
Lucia and Hiro have one of my favorite RPG romances and it isn't one I'd consider replacing with this pairing, but it's a close enough second that I figured I'd include it, just in case Hiro, you know, ever decides against completing the epilogue.
Mass Effect
Shepard / Garrus
You know something, I should hate this pairing, I really should. I felt the romance dialogue in Mass Effect, in general, was awful, abrupt, and unnatural, especially at the start of things, and Garrus' was no exception. What was good, however, was everything else about the pairing, and the romance between them, born from trial, trust. and friendship, feels natural enough that even squirrely dialogue and divergent species can't kill it for me.
Breath of Fire II
Ryu / Nina
ae0dbfe2f0b73963b99d2bf8b6e22baa.jpg
Some people like Ryu / Katt, and I kind of see it, but this was always the pairing for me. Nina's generally on the quiet side with her emotions, but it's pretty (undeniably) clear she has feelings for Ryu, and I like to imagine they are reciprocated -- especially if Ryu I / Nina I are any indication. Sucks for that Wing Clan bloodline, though.
Suikoden V
Prince / Lyon
I don't think Lyon wants this to be romantic. But we all know it is. >:3 Theirs is a romance eclipsed only by . . .
Georg Prime / Cheesecake
Even a decade later and a continent away, this man and his cake remain inseparable.
The Last Blade 2
Kaori 'Kojiroh' Sanada / Washizuka
lb2-art5.jpg
While I've never found anything to official imply anything between these two, I've always paired them together in my head. While this may be due to their similar fighting styles and outfits (both being part of the same military squad), Washi also knows that Kaori has assumed her brother's identity at the head of the squad following the events of the first game and both keeps her secret and follows her loyally. I generally like to assume there is some romantic attachment there.