The story was fine sans the ending.
You hate almost everything anyway, Neon.
Sure perfect sense. Who was it that revived you again? And what did he do to keep you in check? Ohh that is right, the start of Mass Effect 2 is also made of nonsense
Cerberus or more specifically The Elusive Man, who did so because they/he knew that Shepard was really super-duper cool (which if I recall correctly the developers actually wanted you to feel, it's why they gave you the ship to control and why you were always the one leading, they made Mass Effect to give you the power trip.) and without him, the entire united federations of the galaxy would be caught in too much Red-Tape to do anything.
And the way he kept Shepard in check was by exploiting his natural goodness, he pointed out horrible atrocities that the real Shepard could never have left standing, gave him a slap on the bum and off he went, in fact, The Elusive Man was right in not putting a mind-control chip in Shepard, because he teammates probably would have found out, Tali, Legion (assuming they wouldn't have mind-controlled Shep into selling him), Ms. Doctor Lady when he went for a checkup, they all would have figured out and they would not have been happy.