A quick look at the numbers is all anyone needs to prove their point that Rodgers is clearly a superior quarterback. In 2008, after taking over the full-time role from Brett Favre, Rodgers posted an impressive 93.8 QB rating. He threw for 28 touchdowns, nearly twice as many as Smith's highest total from 2006 (16). In Rodgers first full year, he threw for over 4,000 yards. Smith has yet to break 3,000 yards in a season, or even 300 yards in one game. (For the record, Rodgers has six 300-yard games in 25 games.)
There is one major caveat to all of this: Context. The book on Smith coming out of Utah was that of a promising, young athletic quarterback who had some issues with his mechanics, but had a high ceiling. While Rodgers was the more NFL-ready quarterback, despite looking robotic in his delivery. Smith was the project, Rodgers was more plug and play and yet, the 49ers waited just 5 games before submitting Smith to the NFL-wolves.
While Smith was enduring the growing pains that any young quarterback will endure, Aaron Rodgers was riding the pine behind perhaps the best quarterback in a generation. Rodgers absorbed and learned how to play quarterback at the NFL level from Brett Favre, a man that - at age 40 - can still throw a dart through the heart of opposing defenses. Alex Smith had 5 weeks to learn the NFL from Tim Rattay, a quarterback who peaked in week 9 of the 2003 NFL season with a win over the Pittsburgh Steelers.
Many quarterbacks survive in the NFL without an adequate role model. Joe Montana had Steve DeBerg. Peyton Manning had Mike Quinn and Kelly Holcomb. Both of the preceding quarterbacks also existed under one offensive system, illustrating the importance of continuity. Rodgers has only ever had to learn the West Coast offense, first under MIke Sherman, then under Mike McCarthy. That's like driving a Ferrari after learning on a Porsche. Alex Smith has never had an offensive coordinator for more than one season since college. And he had to make the switch from McCarthy's West Coast offense to the Coryell number system in 2005. That's like driving a Ferrari, then switching to a Ducatti while learning to switch-hit. Between different terminology, systems, coaching styles, and formations Smith has never had time to learn anything but the surface of an offensive system.
So let's say we throw out the system changes and the time spent maturing on the sidelines. Rodgers still has a more talented roster in Green Bay than Smith has with the 49ers. With Donald Driver and Greg Jennings, Green Bay has a strong set of starting wide receivers. In other words, Rodgers has receivers better than Brandon Lloyd to throw to. Green Bay also has a strong running game, with Ryan Grant leading the charge. While the team is only averaging 77 yards per game, they are ranked 8th in the Football Outsiders DVOA (Defense-adjusted Value Over Average) rankings. The rankings take note of how much more effective a given play is based on the average gain in similar situations league wide. More can be found here.
When you take these three factors, time, continuity, mentors and talent, it's easy to see that Rodgers was drafted to a team with a favorable situation for a quarterback that needed some developing. If you put Rodgers on the 49ers in 2005 and ask him to carry the team he would fail, just as Alex Smith has. If you took away Rodgers receivers and asked him to win games he would not win as many. If you changed systems on Rodgers every year he would not look as polished as he does now.
Everyone who says that Nolan and McCloughan missed by drafting Smith first overall miss the critical component to everything: context. The fact is Rodgers may or may not have been a better quarterback on April 23rd, 2005. He is a better quarterback now not because of the player he was in 2005. Rodgers is a better quarterback now because he was drafted to Green Bay and not San Francisco.