I'd say the Reaper base at the end of Mass Effect 2 made me think for the longest. However, the difficulty of the choice is due to the unknown repercussions which will presumably shape Mass Effect 3.
I mean, all things considered it's much better to save the facility, and yet for some reason they made that a moral decision when there was no believably good excuse not to keep the facility. Supposedly it's now in the hands of Cerberus, but Shepherd knows where it is, and undoubtedly the Systems Alliance has the power to take control of it. Just all round a dumb idea. But the choice is perplexing.
I mean, all things considered it's much better to save the facility, and yet for some reason they made that a moral decision when there was no believably good excuse not to keep the facility. Supposedly it's now in the hands of Cerberus, but Shepherd knows where it is, and undoubtedly the Systems Alliance has the power to take control of it. Just all round a dumb idea. But the choice is perplexing.