Family
You can never know another, even your father
A common thread running through both Fran and Balthier's pasts is the severance of familial ties. Fran effectively abandoned her sisters when she turned her back on the Wood, officially cutting free upon her return with the main party; "I am as them now, am I not?", she tells Jote. "Good-bye, sister".
Similarly, Balthier's stint as a run-away has everything to do with his sour relationship with his father, Dr Cid. Such a relationship -- like the doctor himself -- is never spoken of as being of the fatherly kind. Balthier addresses the man by his given name and doctoral title, referring to his familial ties as part of the all-encompasing (terrible) "Past".
Although we are only given brief snitches of insight, we can deduce that Fran and Balthier have entrusted enough in one another to find a common ground in their individual woes. Even if specifics are unknown, we know they form their partnership on the basis of being outcasts. However, once the party reaches the Pharos Lighthouse, the idea of family is shown in a different light.
As father and son face each other for the last time, Dr. Cid offers the last word:
If you are so set on running, hadn't you best be off?
Balthier turns to leave; however, he is stopped when Fran collapses under the strain of the Mist. He kneels beside her, and she advises him in a quiet tone not unlike that of his father's:
Hadn't you best be off? That's what a sky pirate does. You fly, don't you?
Balthier leaves, only this time with a weakened Fran in tow.
Already touched upon in the romance section (which you have undoubtedly already browsed), the duo's exchange in the lighthouse is a definitive moment for the pair, and its timing is perhaps more significant than the physical intimacy discussed in the aforementioned romance section. In posing back-to-back, near-identical questions from two very different characters, Final Fantasy XII is asking us to compare Balthier's reactions. Where he turns from Dr. Cid willingly (albeit grimly), he remains firmly at Fran's side. Clearly Fran is more important to him than his own flesh and blood.
Balthier's decision adds another spin to Fran's previous statement of being "of them now" when leaving the Wood. Although she does not hold the same disdain for her sisters Balthier holds for his father, she still identifies with the humes more than her native viera. Moreover, she identifies with Balthier more than her native viera.
Of course, family is not the Big Theme in Final Fantasy XII like it is in the Compilation of Final Fantasy VII, and it shouldn't be treated as such. However, it's worth noting that the same story that depicts Balthier and Fran as sharing more familial affections than their own kin later reveals that brotherhood is all that binds Basch and Noah. Under the overarching theme of loyalty, blood is an idea that's put on the table but not fully explored; honestly, I'm not sure what to take from it right now.
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