Now that Alex Smith has completed his first full season under Jim Harbaugh, let’s break down what we know about his game at this point in his career.

Here are his top-five strengths and weakness.

Strengths

5. Following directions. Smith does everything the coaches ask him to do. He stays at the practice facility late on weekdays game-planning with the coaches. He led mini camps and taught Jim Harbaugh’s playbook to the offense during the lockout when he wasn’t under contract. During games, he executes exactly what the coaches tell him. Harbaugh explains the reads to Smith in his headset until there are 15 seconds left on the play clock and communication stops. Look at this guy, and if he’s not open do this. And Smith does it. At Utah, Smith ran Urban Meyer’s offense as well as anyone ever has, throwing 32 TDs and just 4 INTs as a 20-year-old junior. As a 22-year old 49er, he threw 16 touchdowns and won 7 games for offensive coordinator Norv Turner. And just this past season, he sometimes looked like Andrew Luck running Harbaugh’s offense, throwing 17 touchdowns and just 5 interceptions.

4. Mobility. For a tall, drop-back pocket quarterback, he can run. Since his arm is somewhere between a B+ and an A-, he’s best when he rolls out of the pocket. In the red zone, he’s a threat to run for a touchdown when he rolls out – he scored the offense’s first touchdown of the year that way. He’s quick enough to run the option and designed quarterback sweeps. He ran about three times a game this season. He should run more in the future.

3. Toughness. He’s physically tough: he can take a shot and not fumble the ball. He can take a crushing shot and pop right up and jog to the huddle. He’s cranially tough: He played half of the Cowboys game with a slight concussion. And he’s mentally tough: He didn’t leave the 49ers in free agency for a “fresh start” and a “change of scenery,” like his family and most people thought he should have done. He came back to San Francisco, the same city that booed him off the field in 2010, and won 14 games and became a hero. That’s extraordinary toughness.

2. Prudence. He hangs on to the ball tightly with two hands in the pocket. He doesn’t throw risky passes that could be intercepted. In his entire college career at the University of Utah he threw eight picks in 587 pass attempts. At his best, he’s the king of not turning the ball over, but for most of his NFL career he turned it over a lot, throwing more interceptions than touchdowns. This past season, Harbaugh helped Smith rediscover his prudent, efficient nature as a quarterback.

1. Fourth-quarter comebacks. As much as prudence worked for Smith in ’11, he played his best when he was losing late in games and he had to throw the freaking ball to win. No thinking, just throwing. Everything people said he couldn’t do physically – throw accurate deep passes, make stick throws into tight windows in the end zone – he did to win games. There was the perfect throw deep down the sideline to Michael Crabtree in Seattle. And of course, there was the game-winning touchdown throw to Vernon Davis in the playoffs to beat the Saints. He can become an elite quarterback if he makes those throws more often and more consistently in the future.

Weaknesses

5. Improvising. He always seems to look for one option downfield, and if that receiver isn’t open he immediately throws to a check-down receiver for modest gains. When he scrambles, he usually throws the ball away. His best improvisational move is to take off and run. He is not wired like Aaron Rodgers or Ben Roethlisberger, who scramble around behind the line of scrimmage and wait for receivers to get open outside of their routes. Smith has the athleticism to do that, but he isn’t comfortable with chaos like those other QBs are. It’s not in his nature to improvise.

4. Sacks. Smith has played a full 16-game season twice – in 2006 and in 2011. The main difference in Smith’s stats between those two years is he threw 11 fewer picks in 2011, but he took nine more sacks. It seemed all year that Smith made the conscious choice to take the sack rather than force the pass into coverage. But sacks are bad, too. The offense loses yardage and the down. It’s rare to score a touchdown in the same drive in which you take a sack. Throwing an interception isn’t always bad – it can function as a long punt. Smith needs to figure out a way to take fewer than 40 sacks in 2012, and that may mean throwing a few more interceptions.

3. Field vision. The first play of the Harbowl encapsulates this issue for Smith. His primary read was Vernon Davis in the flat. He was open. But, so was Delanie Walker sprinting deep down the middle of the field uncovered. Smith didn’t see Walker because he wasn’t looking at the middle of the field – he was focused on his primary read down in the right flat. He completed the pass to Davis for a three-yard gain instead of to Walker for a touchdown. In Smith’s mind, he was throwing to Davis all the way unless he wasn’t open. The best quarterbacks (Aaron Rodgers, Eli Manning, Drew Brees) don’t think that way. They look at the field and quickly identify how to make the most out of each play.

2. Third down. You can almost read his thoughts as he lines up in shotgun on third down and long – I will not throw an interception on this play. He usually doesn’t even throw passes that cross the first-down marker. He checks down to Gore or Davis or Crabtree and asks them to break tackles. Or he throws the ball away or he takes the sack. Eli Manning can look left, right, then left again, manipulate the safeties, create a little window and throw a 20-yard rope on third and long. He does this routinely. Smith will never do this. He doesn’t have the arm-strength or the temperament. For the Niners offense to improve on third down they have to get better receivers and Greg Roman needs to call better plays, and Smith needs to be more adventurous.

1. Passivity. He’s the most passive good quarterback in the NFL. He’s only aggressive when he’s losing and he has no other choice. He couldn’t be passive against the Saints – Drew Brees kept throwing touchdowns in the fourth quarter. Smith had to keep bringing the Nines back, and as a result he made the best throws of his life. Against the Giants in the NFC championship game, he hardly trailed in the fourth quarter, so he wasn’t forced to not be passive, so he took sack after sack and the offense punted and punted and punted. He’s good when he’s aggressive. He needs to be that more often, not just when the game gives him no other choice. His passivity lets opponents hang around, and then Kyle Williams happens. Smith will never be elite as long as he’s passive. He needs to be the aggressively prudent quarterback all the time.

I’m leaving for Mexico tomorrow. Back at you in a week.