The plans of Eru regarding His children were not always clear.
The Valar had been given specific instructions in some matters; not so in others. One such ambiguous matter was marriage between the different Children of Illuvatar. It was never forbidden, but was widely regarded as unwise. The differences between them - their nature; their lifespans, their fates after death - were immense. Such pairings were considered profoundly unequal and likely to end in sorrow.
Nevertheless, these rare unions were permitted, and often uniquely blessed. These couples' destinies were often bittersweet, but their lives became defining events in history; their legacies echoing throughout the ages. They were symbols of hope, of unity between peoples.
Beren and Luthien.
Tuor and Idril.
Earandil and Elwing.
Arwen and Aragorn.
Jake and Neytiri.
In many such unions, Eru offered a solution to the inequality: the couple would be allowed to share one nature, one fate. Tuor and Idril were granted the fate of the Eldar. The elf Arwen chose the fate of Men to be with Aragorn.
Yavanna never ceased believing that Eru wanted His children to live together, to share the world. It was the sorrow and corruption Morgoth brought to the Earth that stood in the way of this. She had always longed for a day when the separation of peoples could end. It may have been too late for humans and elves; but she held high hopes for the future of humans and Na'vi.
When the two peoples first met, she was hopeful. Her hope quickly turned to sorrow at the violence and suffering that followed. But now, years later, hope stirred again in her heart as she considered the prospect of two unions between the peoples in two successive generations - a monumental, auspicious event that had not occurred since the First Age.
But how could it happen this time? It was not like with the Elves. The bodies of the Secondborn and the Thirdborn were very different. Though their fea were so similar, the songs of their hroar were written in different languages. They could not breathe the same air, or eat many of the same foods. For Jake and Neytiri, a solution had already been present - the artificed body that Yavanna guided the man's spirit into after he had made the choice. But the human boy and the Na'vi girl she saw now did not have that option.
Yavanna knew it was not her place to make different bodies for the Children of Illuvatar whenever she wished. If these two did indeed commit to each other, would she then be permitted to grant the young man a new fana? The situation was unprecedented. Would Eru do it Himself? Would the human solution become available? Or would they have to remain as they were?
For now, she supposed, there was nothing to do but wait and see what the future held.
AN: The challenges faced by Human/Na'vi couples are not unlike those faced by Human/Elf couples. Both are people who can love each other, but they have very different natures that have to be reconciled somehow. Even after they come together, their former natures and their worlds may clash, and their stories won't always be happy-ever-after. It's a dilemma not only for the couple in question, but also for their loved ones, their societies, and the Powers who must be very careful about getting involved.