In fanfiction, the possibilities are nearly endless. Regarding Edward Elric becoming a homunculus, it could be a very interesting concept. If he were to become one, it would completely change his relationship with other characters. For example, his brother Alphonse might react in a very different way. Also, Edward's own view of himself and his abilities would be transformed. His struggle with his new form, if it were to happen, could be a central theme in the fanfiction. Maybe he would try to find a way to reverse the process, or perhaps he would embrace his new existence as a homunculus. It all depends on the creativity of the fanfiction author.
One possible plot for 'naruto is a homunculus fanfiction' is that Naruto is secretly a homunculus created for a specific purpose, say, to be a weapon in a long - forgotten war. As he grows up, he starts to show signs of his homunculus nature, like enhanced physical abilities or strange powers that are not part of normal ninja training. He then has to figure out who made him and why, while also dealing with the fact that some in the ninja world might see him as an abomination. Along the way, he could meet other homunculus - like beings or discover ancient secrets about the connection between homunculus creation and the ninja arts.