I haven’t played too many games where there’s a couple, let alone one you get to see much interaction from. I’ve heard of Link / Zelda and Mario / Peach brought up as examples. They fall into that set of not much interaction. Tidus and Yuna from Final Fantasy X is my choice. There’s a real love story there and we see them both grow as people. It’s probably the first love story I’ve seen in a game, where it’s not all about rescuing the helpless damsel from peril.
The Diary of an Evli Genius 