Unfortunately for McCain, the comparison is easy and decisive: Obama has run a far, far better campaign by essentially every measure. Furthermore, Obama put his campaign together from scratch with no help from the Democratic establishment in the first year and a half, whereas McCain had the Republican party behind him until he ran out of money temporarily before the primaries.
Make no mistake, Obama has run a far better campaign. He is better organized, has more volunteers, they are more enthusiastic, he has raised far more money, he has raised money from far more people, he has registered more new voters, and he has run a strategically consistent campaign from the beginning while McCain has a new strategy every couple of days.
Although Obama is perfectly capable of going negative, he does so far less than McCain, and usually only in response to attacks. The polls say Obama won all three debates. Then there's the single most important decision of any campaign, who will be vice-president? Obama's pick for VP was boring and safe, but there's no question Biden is knowledgeable, whereas Sarah Palin clearly knows very little about national and international issues and, worse, seems to have little interest. Many intelligent, notable conservative Republicans, e.g., George Will and General Colin Powell, have called her unfit for the job.
In the one apples-to-apples comparison of executive performance we can make there is no question: Obama is better than McCain by a wide margin.