125 hrs? You must have went off to disco or something in between somewhere. Several times. Or you're simply unused to Bioware's style and are over thinking things. For hours. I never checked my hours for the first run but they can't have been more than half that.
Wittiness aside, the choice, if present is binary throughout the game for the most part. You either side with one side in the conflict or side with the other. Whichever side you choose, you'll progress with the storyline. Now, I've heard there may be a third option somewhere, but I haven't been able to make it work. I'd suggest hanging around on their official forums, there have been threads from people sharing their various experiences with the games, and I'm sure you'd find answers to what puzzles or disappoints you