His first year, he was so raw he didn't even know how to drop back from the pocket correctly so I think that year wasn't really a good measure either. All-in-all it's hard to say anything about Smith because we are judging one year of production from two years ago.
But we can say this. Alex Smith has shown plenty of flashes of the tools that he brings to the table. He has a good frame, good height and has continued to gain weight since getting in the league. He is athletic with a pretty strong/accurate arm and can throw well on the run and has pretty good escapability. Most importantly, he is a hard worker and has always put in the time and effort to learn the 4 offenses and study film (ever OC has said so). A lot of QB's have a limited ceiling due to lack of athleticism, intelligence, work ethic, etc. Smith doesn't have those limitations, so thats why there is still A LOT to like about what he brings to the table in terms of his tools.
The two areas which he has struggled - mechanics and reading his progressions quickly are things that most young QB's struggle with. All of his offenses have traditionally been timing offenses, the WCO and the Air Coryell don't throw to open WR's as often as the spread offense, without good mechanics it makes these timing routes nearly impossible. However, under Turner (who worked tirelessly with his mechanics, Smith really improved in this area. We should expect a similar effect with Martz). Reading progressions faster should come with more experience in a single offense, if he ever gets the chance.