I think it was (perhaps still is tbd) a complete clusterfuck of things. At the same time I do think his 'struggles' are overblown.
It was beyond just an inefficient playcalling system. There was no coherence in the offense. One down we'd have 5 wide the very next we're in the pistol in a read option with 2 TE, and 2 RB with 2 WR. The next we're sending our full back on a deep route. That was just the playcalling system but just a shitshow overall.
When your perennial Pro Bowl LT blames "scheme" as an issue you've got a problem that's not the QB's fault. There needs to be coherence in the offense to find a rhythm. We never had that with Roman/Harbaugh at the helm. We as fans questioned the fuck out of it with "Why did we abandon the run?"
Play design has been one of our largest issues. Remember the drop by Vance McDonald in the endzone because Davis was also there? Crabtree and Moss had the same thing happen to them a few times. There was an occasion in 2012 (I think it was against the Pats) that I saw Kap almost blow a timeout so he could tell Jenkins where to line up.
This is why we would hear so frequently from Kap that we just don't know what his reads where, while we bitch that he's a one read QB. Our hopefully now former play design did him no favors. He needed a fuckton of time for our collection of vets (who started over the younger guys because they could grasp the playbook easier) to run the convoluted play design. The offensive line at times didn't know what was going on or just plain sucked as shown by Boone just flat out missing blocks on occasion.
Now Kap didn't fully help himself because he does have legitimate issues. His footwork and pocket presence combined with his ridiculous pause in his windup did him no favors. This is how Sherman has Kap's number. He studies our shit routes then does nothing but run the route and watch Kap and jumps the ball due to the pause in his windup.
Don't think it's inadequate emotional maturity but more of a psychological block that Kap needs to overcome. Relieve that pressure and just play the game. He needs to stop forcing things and beating the shit out of himself for everything.
Harbaugh being gone is an extremely good thing in some regards. Watching numerous press conferences Jim would leave Kap to the wolves to own all the failures. Harbaugh would avoid and dodge negative performance questions for everyone but Kap. We all know the Kap press conference "I gotta play better, we gotta make plays, just have to execute better".
That shit was translating on the field. Someone drop a pass? You're not making plays so I'll try to force the ball instead of scrambling for 10 yards or checking it down.
That talk of needing a teacher or a mentor for a head coach leads to here. Kap needs that break and support to be successful. Rather than shouldering the world he needs more faith in his offensive line (to avoid the ghosts and help his footwork), to rely on his receivers to be where they should at the right time and not drop the fucking thing. He needs to grasp that you don't win the game on every play, and instead take it as it comes to you. Game and situation awareness he needs coaches to help him rather than rush with 15 seconds on the game clock while you wait for 2 shifts and a man in motion before audibling.