First off, you overestimate the control any of us have over events that happen in our real lives. It did not strike me as odd that the twists and turns in the story were happening without my being able to control them.
Most of the time, the responses I gave to options were close to what I would have done "in that position". Working for corporations my hold life trains you to react with 'the right" answer and not some emotional kneejerk, so it felt "real" to me.
Interesting view. In my opinion, I feel we all have a free will to do as we choose. I agree with you that what we "feel" may not always be the correct option. However, I don't condone a "going along to get along" method as one may have to do in a corporate situation if it contradicts the truth. The truth is the truth even if noone believes it. A lie is a lie even if everyone belives it.
There are times in many of the storylines where you may have someone you think is close to you betray you. And you don't always have the option to deal with the betrayal as you may react to it as it happens. There are times in the story where you choose an LS option that doesn't seem to be very "good" and an DS option that doesn't seem to be very "bad". There are many times where LS and DS options are basically a bit of grey moral relativism.
In the end for me, the story doesn't feel like mine and to be honest both sides of the conflict in this war are pretty reprehensable. The empire is machiavellian on steroids and the Republic is just out and out right corrupt. I don't feel for either side.