Being that it's fake news, it's inevitable that the show's going to dump on anyone in the public eye, liberal or conservative, so while I can clearly see Stewart's leanings towards liberal the show itself clearly makes fun of everyone...
I watch it every night, and they really don't pick sides IMO... Of course Bush is going to take a little more flak at the moment, just as Kerry would if he were president. The show has always been that way in my view.
As far as Stewart Vs. Kilbourne, I think it's a matter of opinion, but the show's never had the success it has now under Kilbourne so I'm hesitant to say Stewart isn't legitimately a better host. Kilbourne was good though, so that's a tough call at best.
The ratings for the show are at all-time highs though I guess, it's winning awards left and right, it's considered one of the better shows on TV right now I guess... I can't really complain. I like it as it is... I was sort of fearful with the last loss of reporters like Steve Correll, but the new people are filling in great or even better...
It's one of the few shows I watch every night I'm home, so I'm pretty happy as it is, and hope Stewart's on the show for the long-haul. To me it's a situation of not messing with perfection... Only tweak I'd make is to have Lewis Black's reports on a little more frequently since he's one of my top 3 comics, but I could see where too much "Back In Black" could clog the show up some. Only so much time...
Overall though, I love The Daily Show just fine as it is myself.