Well, based purely on practical concerns (medical advances, technology, women's rights, etc.), why WOULDN'T you want to stay in the present? But I realize the past is kind of idealized in Inuyasha, so I guess it wouldn't matter much either way.

I do agree that she shouldn't have to stay in either place permanently, but the ending pretty much implied that she had totally given up her "normal" life, judging by her family's reaction, her clothing, and so on. I guess it's possible that she's just spending the majority of her time in Sengoku Jidai and not all of it, but still. Seemed pretty final to me.