Smith was drafted rediculously high. Insanely high, in hindsight. He was going to save this storied franchise and the pressure was evident in his play. He was rediculued by fans and berated by coaches. Not many had a tougher road than Alex Smith. Harbaugh instilled some confidence. Alex needed a hug but a the end of the day, IMO, he's just not very good.
Wilson has had to fight his way through everything because of his stature, but nobody really expected alot from him and everyone cheered for him and wished him success. America loves the underdog. Wilson is almost playing with house money. Like Smith, he has the same pressure every NFL QB has, but as a 3rd rd pick, he's likely to get a break from the press (and fans) and the press is more likely to feature him positively when he does well. Not many want to attack the underdog. I think this is a huge difference in the development of Wilson and Smith. One is being groomed and shrouded in confidence, the other was tormented, rediculed and his confidence crushed.
Talent wise? I think Wilson is smarter than Smith and his lack of size has forced him to be more nimble and creative in moving the chains. I also think Wilson has a better arm and a shorter memory.
At the end of last year, I felt SF was a pass rusher and QB better than us. I don't think that anymore and SF, if smart, will keep looking for a QB, IMO.