Was the change from Alex Smith to Colin Kaepernick the only noticeable difference in the 49ers offense over the course of the season?
This counts as the most noticeable difference because any subsequent changes really evolved from this. Michael Crabtree was off to a strong start with Alex Smith, but once Kaepernick took over, it went to a whole new level. Vernon Davis was Alex Smith's go-to guy and we saw Kaepernick looking away from him, and often more to backup tight end Delanie Walker. That changed against the Falcons, but it has still been noticeable.
The biggest change aside from Kaepernick is LaMichael James taking over as backup to Frank Gore. Kendall Hunter was the primary backup, but he tore his Achilles, opening the door for the rookie James to step in. He and Hunter are both speedy, athletic backs, but James seems to bring a little something extra in the speed department, while Hunter was the more physical back. Also, given James' success in Oregon's offense, the change to Kaepernick has helped him adjust to the NFL game.
Vernon Davis did not have anywhere near the seasons he's enjoyed in the past, statistically. Why is that?
It is a mix of reasons. Kaepernick has looked more toward Crabtree as they seem to have the kind of chemistry Davis had with Smith. Davis entered the NFL with less than stellar hands, but he has worked on improving them an incredibly amount. At the same time, it is also likely taking Davis a bit extra time to get used to the speed of Kaepernick's throws.
Davis has not been non-existent, however. He remains one of the better blocking tight ends in the league, and he still draws double teams. This opens the door for other receivers, so even though the numbers don't show it, Davis remains effective in a variety of ways.