In an interview with PC Gamer, Producer Michael Gamble says that Mass Effect 3 will not only end Shepard's story, but will also be the last appearance of the Commander. While BioWare don't have any plans to end the Mass Effect series according to BioWare CEO Dr. Ray Mazuka, what has been confirmed is that Mass Effect 3 will be the last appearance of Commander Shepard. I guess after what the Commander has already gone through, they deserve a break/retirement.
I figured this might be worth sharing.
PC Gamer interivew: here
GameSpot article about the interview: here