Naughty Dog has an excellent history with storytelling at this point. I'd say odds are good that Ellie's relationships with other people, whether romantic or not, would be part of an interesting story.
However, if anyone objects to Ellie relationship preferences being a focal point of the story, I'd be curious to hear thoughts on Uncharted 4 emphasizing Nathan Drake's sexual orientation by going into such detail about his marriage and relationship with his wife, Elena. Uncharted 4 even devotes an entire chapter to just being around the home with two heterosexuals acting so overtly heterosexual.
Quite edgy.