The biggest is that Obama is the incumbent President. This not only puts him in the role of President - and we saw this week how that helps, it means that people KNOW him and Michelle. It is far harder to redefine a person that everyone has seen up close for 4 years.
In 2004, the SBVT would have had NO impact if Kerry were the sitting President - just as it had no impact on his race in MA in 2008 where everyone knew him. In fact, that is why even if the Bush AWOL story were more mainstream, it would not have mattered. The NYT polled people in 2004 at the beginning of the Rather story. The result, of the people who in an early question said they would vote for Bush, NONE answered that they would change their vote if the charges were true. Those charges could have had a big effect in 2000 - but by 2004, the important thing was his time as President.
The other thing is that Obama has FAR more money, where Kerry had the same amount as Bush - but needed to stretch it over 13 weeks vs Bush's 8 - an unintended consequence of the McCain/Feingold rules that were implemented for the first time. (this plus the 527 ads that put out negative ads that the helped candidate could righteously deny that it had anything to do with them - even if they share a lawyer with Bush/Cheney.)
This year has been terrifying because there is an essentially limitless amount of money spent against us. In addition, the RW echo chamber is still there - and even parts of the media that were not clearly RW have treated Romney with kid gloves. Imagine if the story of cutting the fellow student's hair having been done by Obama 2008, Kerry or Gore. Do you think any media person would have excused it because they were young? Not to mention Gloria Bulger (CNN) actually speaking of the dangers that Mitt faced in France in 1968. Not to mention, there were some in 2004 who actually repeated RW criticisms that Kerry's injuries were not bad enough to deserve medals!
It looks like Obama will win -which will be incredible versus what was against him. But, a reflection should be made that it should not be this close given the fact that Romney is an awful candidate. The really scary thing is that we won't have the benefit of incumbency next time. (unless Hillary runs - who you can think of as a past incumbent to some degree.)