I was just about to play though one and two again when three was announced. Now I can't bring myself to do it as I want my Shepard to finish her journey first. I don't want to start playing it again and like my new Shepard more! 
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He's back to being a Spectre/Alliance man again.
Shepherd is not now, nor has ever been, a man. I don't know who the dude traipsing around in the commercials is; a jerk, most likely.
And why would Cerberus now be out to kill Shephard?![]()
What if you handed over the base to Cerberus, tho?
And the second bit would be really petty in whole scheme of things.
Perhaps the technology backfires eg indoctrination.
True, but TIM isn't exactly a nice guy (I'm going to call bull on the idea that Jack was the result of a rogue cell). Not to mention the thresher maw experiment, assassinations, bombing a Quarian ship etc. Those kind of events fit with the ends-justify-means character we get in 2.
Eh, don't get me started. Loads of stuff I'm itchin' to see how they address in ME3.