She is woman of a race that is not widely known to the world. A race, called Viera, that strives to isolate itself from the rest. Fran however walk among the humes and even spends all her time very closely to one of them. A man. Balthier.
Balthier: "Fran is special in that she'd deign to partner with a hume."
Fran: "Oh? Like a sky pirate that chooses to steal through the sewers?"
Balthier yet again just pointed out that he is the leading man
Fran: "I'd say you're more of a supporting role."
Balthier: "Fran, please."
Often words are not even neccessary for the duo. At many occassions we see them simply giving eachother a look, as if they know exactly what the other is thinking. Fran reads Balthier's feeling very well, but I believe it's not because of any born senses of the Viera but rather that she knows him very well.
We don't actually get much background on how they came to be partners but we can sense that they have been together for a long time. They've come to trust eachother and one would never want to leave the other's side. Whether it be love or simply companionship, these two hold a mutual understanding like no other. They have much in common, one thing being their relationship to their pasts.
Both have cut all ties to their past and there will never be any turning back in either of their cases. Before meeting they were practically alone in the world.
Nothing is confirmed to us in the game but whichever name their relationship takes, it is beyond friendship. They are family. They watch eachother's backs and one can always fall back onto the other.