Pete,
I guess we'll never know if he wouldn't have been re-elected. I think he would have been but who is to know, particularly because the trend at that time was to have only one term Presidents (for the most part). Also, I don't know if the country would have entrusted the future to McClellan (thank goodness).
Regarding whether he was a great war president, I believe some scholars do believe that he was and I know that James McPherson has a book coming out about it in the Fall. Just as now, I don't know if we can rely on the man in the street to give us a good feeling about situations.
Based on my recent reading of Team of Rivals, those who came in close contact with him and who underestimated or depreciated him initially usually came away with a different opinion over time.
Had he lived I believe his aura would have been enhanced in his reconstruction efforts. Unfortunately, we'll never know.