One of the things that I really, really love about ME3 is the way our choices in previous games finally meant something more than just a cameo. They actually determined our latitude in making choices in ME3. And it wasn't simply "Paragon wins" either, particularly with the Geth-Quarian dispute where the renegade "kill the heretics" choice was the more optimal choice for achieving peace. So I say: more power to ME3. From my experience with both the ME series and the DA series, it is the only game in the entire BW oeuvre where our choices actually did matter.
I agree with what you say, but there is still way too much pro-Paragon bias present in the game (and the trilogy for that matter). The problem is that for 95% of the game, it's basically ''Pick Paragon to win and max out your reputation meter!''
Being consistently renegade is much worse in the long run it terms of repercussions, EMS, who lives, etc. While Renegades might have been intended as jerks, they should give us a reason not to be Mr. Goody two shoes all the time. And this is coming from someone who plays Paragon all the time.
I want to be burned more often for making a seemingly good decision. One example I can remember is Rana Thanotopis (can't remember exact name). By letting her live, she ends up being indoctrinated and hurting your EMS. The problem is that this situation where being Paragon ends up with negative repercussions is very, very rare through the trilogy, and in that case it had a very minor impact. And the example you gave is actually debatable in terms of Paragon and Renegade, they could easily have been switched. Is it better to have your personality and identity rewritten than to be destroyed? Should Shepard view a rewrite as a positive choice because it may help their fight against the Reapers, or as a negative because it leaves the door open for more Geth to become hostile?
I actually mentioned this to one of the devs when I was at the Montreal Comic Con last September. They said that since the next game was being made on a new engine, they were going to take the opportunity to re-examine all of their existing systems, like leveling, dialogue, etc. I hope they take advantage of this occasion to make a better dialogue system. No need to dump the dialogue wheel, but add more weight and meaning to each choice.