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SecondWar said:

Picking up on a point I made earlier about how Bioware did not make best use of choices made in the previous game, I wanted to highlight two more brilliant opportunities to develop the storyline which were completely overlooked, despite the fact when the come up it looked like the impact could be serious.

Both of these decisions occur in Mass Effect 2, in N7: Lost operative and Arrival. In N7: Lost Operative you find a Cerberus operative and have to recover some encrypted data about Cerberus' operations that is very sensitive in nature and could do some real damage to Cerberus if it fell into the wrong hands. Considering you are effectively at war with Cerberus during Mass Effect 3 WHY was this not picked up? And in Arrival, when you are given the choice of whether or not to warn the Batarian colonists I figured this could have major repercusions in Shepard's efforts to gather allies, but again is barely touched on except for two assignments that involve Batarians on the citadel, and even here that decision doesn't really come into play.

Maybe I should take a break from the game, I feel I just torturing myself over thinking about what could have been.

I believe he didn't really get a chance to warn the colonies.