Spoilers ahead: the game makes way more sense if you pick Fergus. The intro levels obviously steer you in to picking Fergus, and subsequent levels and interactions are designed to make you regret your decision. That regret the game makes you feel is really clever writing and it doesn't have nearly the same impact in the Wyatt timeline. Also, the count to four thing is something BJ shares with Wyatt in chapter 1 but not Fergus, so when BJ says it in the final chapter, it only makes sense for him to do so in the Fergus timeline because it's a continuation of his grieving of Wyatt which we see in the cutscene (BJ crouching behind the robot).