Maybe I just didn't play long enough because I put it down in the 2nd act, but I put 20 hours into the game and never came across a single mission that had long term effects outside of the mission. From what I played, you make choices that can effect to outcome of particular quest lines but the actual impact of those choices have no bearing on what happens outside of that particular questline.
For example, the early mission where you gotta figure out how to get the flathead. They gave you a variety of ways to go about getting it, side with militech or maelstrom, the only difference is your reward at the end. Nether of those groups act any differently towards you regardless of what you chose during that mission.
Again, I've only played 20 hours but I feel like I've done quite a bit of side quest and gotten far enough in the main quest to start seeing examples of these hard choices.