I think I've said this in countless threads about gender in video games, but gender of protagonist aside, it's very very VERY rare when video games script relationships properly. Relationships are difficult to write. Heck, many love adventures (which are all about relationships) are written with by-the-numbers scripting with archetypical characters.
And insert Dincrest's usual spiel about Maya in Septerra Core. Oh, and insert something about the awesomeness of Fear Effect, because that may end up being relevant to this discussion.