I'm not surprised, he can't run Chip's system.
He can't make three reads right at/after the snap. That's what Chip's system is about. In that sense, those three reads are the first option...even if it's three possible plays.
Kaep's head isn't fast enough. The only thing he'll be able to do correctly is run on the read option. He'll get killed.
He's not a one read QB who runs when it's not available. Occasionally he can get to his 2nd or 3rd, but he not consistent at it.
Harbaugh ran safe routes and gave him the freedom to run. His speed overwhelmed defenses who hadn't made the proper adjustments against it.
He's been figured out. He either becomes a QB who can make multiple reads consistently fast, and deliver the ball on time and accurate... or he goes to the bench to be a gimmick. If not that, then he's out of the NFL.