Yes it does change the story. Not the end of the story, but it changes aspects of the story. In one decision, the Vulkars are wiped out. In another, they're not.
My point was that people say that NOTHING they did changed the story, because they expect every little action to change the FINAL outcome. That's a completely misguided notion. Certain actions changed certain aspects of the story, and that's exactly how it should be. I wouldn't want the fact that I stole that wraid plate from that widow on Tatooine to drastically change the rest of the story, because that would be rediculous. I thought KOTOR did an admirable job of altering the storyline based on your actions.
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Hmmm its the butterfly effect, you know the one "a butterfly flaps its wings in China, and causes a hurricane in America" or something like that, but not every wing beat would stir up a hurricane only a select 1 or 2! Not every single decision you make has or should have a dire consequence on the games outcome, only a select few things, such as joining or spurning Bastilla (big thing) but a couple of little things that you didnt think relevant (little thing) should be able to snowball, if you get my meaning?