Actually, your comment is a very good starting point for the discussion about coaches and getting the most out of players.
You are correct that the vast majority of Jim Harbaugh's players were holdovers from the prior coach (Singletary). I accept that Harbaugh benefitted from having a lot of very good players, such as Willis, Crabtree, Vernon Davis, etc. However, Harbaugh then drafted and started Kaepernick, who is a better QB than Alex Smith. He also drafted Aldon Smith, a key part of an elite defense.
Now, the 49ers are becoming Harbaugh's team. And as the team becomes more Harbaugh's team than that of his predecessor, it becomes a better team. Further, Tomlin was given a team just 2 years removed from winning a Super Bowl, with a franchise QB, and likely HOF players at WR (Ward) and S (Polamalu). Harbaugh took over a club with a LB'er who is a legitimate candidate for the HOF (Willis), a good TE, a solid OL, but no franchise QB, a questionable receiving corps, a dubious defensive line, and a pretty bad secondary.
Tomlin was given a lot more than Harbaugh. Further, as the team becomes more and more Harbaugh's team, it wins, and wins, and wins, and wins. It does not lose to the Raiders twice, the Browns twice, a 4-12 Dolphins team, etc. Harbaugh is 37-11-1 in his first 49 games.
Tomlin - given a better roster than was Harbaugh, and if anybody doubts that, then your are just being willfully ignorant - was 31-18 in Tomlin's first 49 games.
In conclusion, therefore, Harbaugh has a much better winning percentage than Tomlin, despite the fact that Tomlin was given a team shortly removed from winning a Super Bowl and a franchise QB, while Harbaugh was given a team that had gone 14-18 in the two prior seasons and had Alex Smith at QB.