Living in the bay area i see all of the 49er games and Crabtree is a really good receiver. He doesn't have deep speed, but he is an above average route runner and gets plenty of seperation. He is an upgrade over Jericho Cotchery. I'd rather have him over Torrey Smith, who i think is a one trick pony.
Crabtree hasn't had a quality QB throwing him the football either. As for Kaepernick, I have personally heard come out of one of his starting receiver/TE's mouth that Kaepernick has no rapport with any of the offensive players, and that his attitude is terrible.