But the 49ers aren't who we thought they'd be. They aren't because they aren't nearly as deep or young or talented or angry as, say, the Seattle Seahawks, who under the fun-loving Pete Carroll currently have a stranglehold on "the best team in the league" title belt.
The offensive gimmicks and quirky formations have been stomped to the floor. The brash, prove-everyone-wrong young quarterback Colin Kaepernick has Anquan Boldin, a hampered Vernon Davis and … peanuts.
With Michael Crabtree and Mario Manningham and now promising rookie Quinton Patton out for a while, Kaepernick doesn't have the kind of weapons flanking him the way Peyton Manning does.
(But look who Tom Brady is throwing toward at the moment).
More than virus strains, the NFL adjusts to changes in life, and for the first time in his stellar start with the 49ers, Harbaugh must adjust, too.
The read-option era seems to have passed before it even reached the infancy stage, leaving San Francisco with a dilemma.
Do they return to the power-run team that exceeded expectations under Harbaugh and former Utah QB Alex Smith the first couple of seasons?
Can Kaepernick handle the offense minus three of his best targets? Doesn't look like it.
Those questions will be answered soon enough, but more pressing for San Francisco has to be the lifeless losses at Seattle and at home to Indianapolis by a combined score of 56-10 two games against top-flight opponents in which the 49ers had no answer for anything.
The team that traditionally won the big, prime-time games fell flat. Fortunately for Harbaugh, San Francisco's favorite megalomaniac, the 49ers have a chance to improve to 7-2 in the next five weeks.
Is the magic dried out? Life in the NFL is tough, and in order to become a staple, you need a phenomenal quarterback, a tireless head coach and the league's top talent.
It certainly did last year, when the 49ers were five yards away from a Super Bowl title.