Offensively, the 49ers work everything off of run action and quick passing out of the shotgun. The 49ers are not tricky in any way. Most of the time, you hear about how pro coaches like to run the same couple running plays out of many different formations to give the opponent different looks. This is not who the 49ers are. They use at least six different running plays regularly, and their favorites are different versions of the "power" play. But the 49ers will also use counters, leads, zone stretches, some traps (though they didn't have any reason to trap Cleveland and likely will not trap the Redskins who play a 30 front). The only play the 49ers don't run that the Redskins do is the inside zone play, because they prefer man blocking when the run between the tackles.
The other interesting thing about the 49ers running game is they use a different set of plays for backup RB Kendall Hunter over starter Frank Gore. Clearly the preference for Harbaugh is to use Gore more because of his style, but he tailors his playcalling to Hunter's strengths when Hunter is in the game. That means more stretch, more cutback, more space plays (the zone-counter leg of the running tree over power, which requires a more patient runner). Think 2005 Clinton Portis against 2008 Clinton Portis for the differences.
I don't think it would be right to say the 49ers are trying to protect their quarterback Alex Smith, but I think they are trying to protect an offensive line that struggles in pass protection. The 49ers will run out of a shotgun look, but mostly, they will go and spread you out looking to create an easy read for Smith. A simple four verticals play in the third quarter against cover two on third and long demonstrated how the 49ers can use Smith's strength to go down the field to Michael Crabtree using a simple play that creates a mismatch and carries a low risk of failure. Four Verticals probably isn't the best way to attack the Redskins in third and long, but using almost the same formation gives the Niners a numbers of different routes that can convert the first down.
Furthermore the Niners like to let Alex Smith throw on first down. Even though they are fundamentally a run-first team, Jim Harbaugh understands how to keep the quarterback happy.
To understand how to beat the 49ers offense, you need to understand why they are successful despite weaknesses. The 49ers don't run as much as they do because they are particulary adept at it. They do it because it limits the weaknesses of their passing game. They've done such a good job of it this season that their passing game has been wildly successful while remaining incredibly limited. I think a lot of defenses have gone up against the 49ers under the impression that they have to stop the run and make Alex Smith beat them. This hasn't worked, it has in fact played right into Harbaugh's hands. You have to do two things when you play the 49ers: beat them on 1st & 2nd down, and attack their weaknesses.
The reason the Power O run defines the Niners so well this year is because it's not a play that's difficult to stop -- if you cheat on it. The Niners love to pull guards in the running game, and if you come hard down the line from the backside, you can close the hole and deliver a nice blind side hit to the running back and maybe knock the ball loose. Of course, now you aren't playing your assignments correctly, and the 49ers can hit you on some plays where it really hurts. You should let the Niners come at you with a power running game. It won't pay off in points so long as you win the field position battle, and you tackle the running back.
But the 49ers can be patient with their running game and protect their offensive line for two major reasons: their defense and their special teams. This team really is the Rex Ryan Jets, or at least who those Jets aspire to be. The 49ers do a fantastic job attacking your protections with just four guys. They have a great package of rushers, but it's also a credit to their scheme: unlike the Redskins who will show an overload and try to bring more guys than the protection can handle, the 49ers will use a stunt to make your young players miss their reads. That means rookie LG Maurice Hurt will likely face pressure on both sides most of the day, and the 49ers will also try to attack the running backs with Tim Hightower out. If nothing else, we will know by the end of the day how well Ryan Torain and Roy Helu understand pass protections. And that doesn't even get to the hilarious mismatch that Jammal Brown will face against Justin Smith. If the Redskins try to win via the play action pass, they will lose this game before the 15 play script has been exausted.
If the Redskins actually let Roy Helu run the ball to get the 49ers out of their stunts and force them to be more vanilla or even run blitz, there's no specific reason why the Redskins can't win this game. You can't beat a guy like Justin Smith, but you can frusterate him into being a non-factor on the outcome. If the 49ers spend the whole game hedging against being run on, there will be plenty of seams in the defense that open up. Redskins Hog Heaven can attest at how good of a cover guy Carlos Rogers is, but the secondary around him is very pedestrian. The 49ers knew they had a huge problem at the safety level. It is still there. In general, the front seven is too good to allow a consistent assult on the back seven, but even Jesse Holley thinks there are plays to be made if a coordinator is aggressive enough. The key for Kyle Shanahan is to remain aggressive, but in doing so, to not forget that he's facing a major mismatch at the line of scrimmage. There has to be a threat of a cutback run consistently for John Beck to enjoy any shot at success.
The 49ers lack any sort of depth on their D-Line, so their front three: Isaac Sopoaga, Smith, and Ray McDonald, must stay healthy all season. Like the Redskins, this front gets a lot stronger in passing downs, gaining premier pass rushing rookie Aldon Smith and package DT Ricky Jean-Francois, and losing the immobile Sopoaga. As far as nose tackles go, Sopoaga is a good one, but the Redskins are far better off with him on the field than with him on the sideline. When he's on the sideline, the Redskins should trap and try to create a big running lane in a non-running down and distance. Having Kyle Shanahan as your coordinator gives this a zero probability of happening, but it's a good idea against the opponent nonetheless.
The truth is that this is actually a good opportunity for the Redskins to win in a huge upset because the 49ers win formulaically, not because they are consisently more talented than their opponent. We know that interceptions regress to the mean over time, and we know that Alex Smith can give away a game just as efficiently as the next guy, but to have this opportunity, the Redskins will need to be the 49ers: patient to a fault. Fortunately, that's exactly who Mike Shanahan always wanted this team to resemble. I think there's a good chance his job may depend on his ability to rally the troops this week. It's not that a firing or change of organizational direction is immenent, but here's a team the Redskins have handled of late, who has turned into one of the better teams in football simply by being more disciplined than their opponent: the Mike Shanahan model. If the 49ers cross the country and look like the more disciplined, better coached team, I don't see what will be different a year and a half from now when Shanahan is 60.
Jim Harbaugh is probably overrated as a head coach due to early success (remember Josh McDaniels?), and if the Redskins win this week, they'll likely make it look like the Denver game from 2009. They'll expose the defense of the 49ers for the second time this year, and they'll dominate the OL of the 49ers, limiting them, and forcing Harbaugh to uncharacteristically break script. The fact that the 49ers come straight at you really limits the excuses. This is not a game that is likely to be decided by one or two plays. It's likely that the outcome has already been determined during the practice week. Either the Redskins are prepared for an opponent they can handle, or they have failed to prepare adequately and no amount of time in the future will cover the gap in coaching between these two teams.