What massive plot holes are you referring too? Lack of closure? Are you pissy because it didn't have a sunshine and rainbows ending where everyone lives happily ever after?
First off, I'm not being "pissy". I'm saying that if they let the publisher write script again, I'm not buying it.
Secondly, It's a shooter game. How about the lack of a final boss battle? You pick curtain 1, 2, or 3. That's it. And nothing you did in the prior two games mattered despite what they promised otherwise.