I recently finished the story for the first time, and wow! This game was and is amazing. But after seeing Bonnie get jealous and watch John and his wife leave, I thought the game was going to keep going; and that Bonnie or Abigail would be a choice. The dialogue of that mission (called Old Friends, New Problems), definitely hinted towards a choice between the two gals. After John died, it was obvious that wasn't going to happen.
Once you take over as Jack I got excited that maybe Jack hooks up with Bonnie, but it didn't happen either. Poor Bonnie :(.
Anyone else think that anything similar was going to happen?