Well, for one thing, Kaepernick himself became a larger part of the ground game. For another, Kaepernick emerged as potentially more than a "game-manager QB," with the arm to hurl the ball, accurately, far down the field. The 49ers, in the midst of a playoff run, took advantage.
But another reason for the ground-to-a-halt has little to do with the quarterback. Remember, Alex Smith himself could run some, albeit not with Kaep's explosiveness. Simply, NFL teams do adjust, and most good teams can stop any one aspect of an offense. Great defenses, like Seattle's, can stop more.
When Harbaugh and Roman first arrived in San Francisco they implemented a run-offense both traditional and innovative. This old-is-new-again approach proved not only effective in itself, but also delightful to watch. Now, NFL defensive coordinators have had two years, and nearly forty videoed games, to watch it themselves. Actually, watching the Ram games alone provides copious clues on how to stop ground-Greg. (Also, many NFL offensive coordinators appear to have watched the Niners, and copycatted their plays, making them more familiar overall.)
What do the Rams, and other teams, do to confound the Niner ground game? A brief summation: shoot the gaps, rotate defensive assignments, follow the pulling linemen, stunt, disrupt blocking angles, reroute runners, tackle efficiently, change defenses, maintain discipline, and in general initiate enough mayhem near the line of scrimmage to stop potential gash plays before they start. Gore often looks frustrated because defenses have learned how to curtail his cut-back lanes. The alternative alleys he once found when original holes were stuffed have closed. In other words, NFL defenders no longer "catch" the 49er blockers; they attack the running game preemptively.
With the running game, however, one should regard the Seattle contest as an outlier. In CenturyLink Field visiting offensive linemen lose one of their penultimate advantages: simply, they cannot hear the snap count, which, in home stadia, allows them to fire off the line of scrimmage a split second before defenders. Neither, in such noise, can offensive linemen work together as cohesively.
Will the 49ers ever again bring the thunder runs that characterized the team during the glory years of the early-Harbaugh era? Probably. Adjustments that did not work amid Seattle caterwauls will work better in quieter times. Also, of course, the 49ers could loosen up run defenses by utilizing Kaep more in his immense capacity as a runner himself. Given the team's legitimate caution in keeping their young star healthy, don't look for them to run this run-risk anytime soon, until the playoffs, or maybe in a must-win game, say the second Seattle contest. (Let's hope they don't lose so much that every game becomes a must-win.)
Ultimately, though, Colin Kaepernick must continue to mature into his full potential. As against Green Bay, he must make teams pay for stacking defenders against the run. He must learn to read defenses more accurately, make better decisions, and develop quicker reactions. Remember, the young guy is still learning the intricacies of the pro game, adjusting to its speed and trickery. This maturation process will not inscribe a straight line upward on a quarterback-skills graph, and will require patience. There will be setbacks, mistakes, frustrations, and, yes, occasional losses. But he's in the right place at the right time, surrounded by folks who want to see him succeed, and with the capacity to help ensure said success.
But Colin Kaepernick cannot by himself rescue the 49er run game. For that, we must turn to the offensive line.
Once upon a time a third-year NFL coach with a young prodigy at quarterback found himself with a team capable of making a playoff run. His team could have made the playoffs simply by passing their way to regular-season victories. However, this coach reckoned that, in order to win when they got to the playoffs, his team would need a balanced offense. So, despite his acknowledged brilliance in drawing up passing plays, the coach stuck with the running game anyway, to the point of risking regular-season losses. In effect, he sent an unspoken message to his offensive linemen:
If we don't run the ball, as well as pass it, we will lose games. If you do not block well, I will let you lose those games. Our quarterback will not come to your rescue, and neither will I. Now block.
Offensive linemen love being given that responsibility. But, in order to practice their craft effectively, they need just that: actual game practice, not just training-camp or practice-field reps. They need to get in sync with each other and with their backs. They need to experiment, adjust, and improve in actual game situations. In short, the 49ers' current offensive line must regain their collective mojo, and during the regular season, so that they will have it in the playoffs. To accomplish that, the coaching staff must have the patience and fortitude to risk losses. Above all, the players themselves must maintain their confidence and commitment, even when the plays don't always work.
By the way, in the aforementioned season, everyone remembers "the catch" made by Dwight Clark against Dallas in the corner of the end zone. What some forget is that, in that late-fourth-quarter drive leading up to the famous play, the Niners mixed runs in with passes. Their offensive line had their mojo working. Harbaugh has watched many game tapes from the Walsh era; let's hope he watches not only for schemes, but for season-long strategy as well.
