Picking either the Youth League or New Yevon makes the story a bit different at certain parts. You can get more percentage toward the 100% goal if you choose the Youth League, but since you like the game so much I would suggest to just pick one, and then when you beat the game play it again on a New Game+ and on that game pick the other side. And since you've already missed some percentage in Ch 1, you aren't going to get 100% on this game anyway, so it doesn't really matter. And also, you shouldn't just go to the Hotspots in each chapter. You are going to miss quite a bit of the story since you did that. You should visit each region at least once per chapter.