SANTA CLARA – Aaron Rodgers was the big loser on NFL draft day 2005. While top overall pick Alex Smith and a host of other college stars shook hands and took pictures with then-Commissioner Paul Tagliabue, Rodgers sat alone in a pinstripe suit, a forced smile on his face and a weary look in his eye.

Rodgers, the former Cal star, was the embarrassed groom left standing at the altar. What's worse, the team that finally came calling, the Packers, already had a special someone on its arm. Rodgers not only lost millions of dollars from his draft-day fall, he would have to apprentice behind Brett Favre for three years.

What we all know today is that, as awkward as it was for Rodgers, Smith would have been much better off in Rodgers' shoes that day. A three-year apprenticeship was what Smith needed. He's not a gunslinger like Favre. He's not street-smart like his buddy Shaun Hill. Smith is a classroom guy. He's a student, a bookworm in high school who went on to earn a college degree in two years.

Throw him into the fire and, in the now-famous draft-day words of college coach Urban Meyer, Smith is "non-functional."

Give him time to master the offense, Meyer said, and "I think he will play in the NFL and be a starter in the NFL for a long time."

The irony is that the 49ers' mishandling of Smith led to a situation that finally gave him the study time he always needed. Smith hasn't made a healthy regular-season start since Sept. 30, 2007, the day Seattle's Rocky Bernard burst untouched through the middle of the offensive line and triggered a chain of events that mostly has kept Smith on the sideline since.

That hit led to two surgeries, worries that he would never throw again and assertions that he was the biggest draft bust since Ryan Leaf. But it also led to much-needed down time.

In the second half of Sunday's game in Houston, Smith showed the accuracy that Meyer raved about the day the 49ers drafted him. That's because Smith has been able to spend more time honing the fundamentals – his footwork, squaring his shoulders – that are critical to playing quarterback.

In Houston, he seemed more decisive than ever. Meyer warned in 2005 that Smith would look lousy and lost until he fully digested the 49ers' offense. Though Smith has yet another new offensive coordinator this year, Jimmy Raye uses a digit-system offense, which Smith has had in three of the last four years. He understands this offense more thoroughly than he has any to date.

The talent around him also has improved.

One of the benefits of being picked 24th overall – as Rodgers was – is that you don't have to endure a rebuilding process. When Rodgers made his first start, he threw to wide receivers such as Donald Driver and Greg Jennings.

When Smith got his first start against Indianapolis in 2005, his receivers were Brandon Lloyd, Arnaz Battle and Johnnie Morton, and his tight end was Billy Bajema. When Smith makes his return as a starter Sunday against Indianapolis, his receivers will be Michael Crabtree, Isaac Bruce and Josh Morgan, and his tight end will be Vernon Davis, who is having a Pro Bowl-caliber season.

Coach Mike Singletary admitted earlier this week he wasn't sure how Smith would play in the second half against the Texans. After all, Smith spent the last two seasons as damaged and as demoralized as any quarterback has ever been.

What would emerge when he finally set foot on the field again? At least the early returns suggest that Smith came through his ordeal more steeled, more prepared and more confident. And that he is a better quarterback than he was before it began.

Read Matthew Barrows' archives and blogs at www.sacbee.com/sf49ers.