This isn't any sort of Earth-shaking revelation, but I felt this needed to be said.
As observed by Brian, stephenrjking and others around here, Shea is risk averse, especially against zone coverage. If he doesn't like what he sees, he won't throw it, and if he feels uncomfortable he'll bug out of the pocket. This has been frustrating to watch, I ain't refuting that. I get it; we have a conservative QB.
However, I don't think enough, if anything at all, has been made of the upside. I apologize for the not-safe-for-lunch image but here's the stat line from Jolton O'Peters, last year's three-headed monster at QB:
185/346, 53.5%, 6.4YPA, 9TD, 10 INT
DSRs were 70, 64, 64, 63, 75, 60, 44, 65, 77, 75, 69, 50. (Average: 64.7)
This is Shea so far:
123/183, 67.2%, 8.3YPA, 12TD, 3 INT
DSRs (pre-MSU UFR) - 77, 77, 74, 79, 68, 87, 68 (Average: 75.7)
The ones he throws are more often sure things, and the YPA is way up, but these are sort of expected with his approach. We're also missing some of the nuances, such as the fact that last year's QBs were hardly fearless. Nevertheless, the takeaway is the TD:INT going from 50-50 to 4:1. Shea's thrown only one pick in conference play and that was off a deflection. He's on pace to finish around 18:4 or so. Also, while it hardly needs to be said that he's an upgrade, "not throwing" is arguably a Bad Read yet Shea's DSR average of 75.7 is comparable to the best QB performances of last season. He's tentative but he'll pass up opportunities to avoid disasters, and that shows in his grades.
I get the feeling Harbaugh has been relying on Shea as little as possible while he works on getting him more comfortable instead of trying to re-write his instincts. If that means leaving some of his potential on the shelf for now, so be it, as long as the ball doesn't go back to the other team. The only thing I'd change in the short term is adding a "two outs" baseball mentality. I for one don't want to see Shea go all gunslinger and start torching possessions, but if it's third and long, as Brian says that's basically a make-it-or-punt situation so that's when he should turn his limiter off and throw it up for grabs -- especially since we apparently aren't converting those anyway.
Still, we should give credit where credit's due; Shea's conservative play has more often than not kept the offense on the field. Just, Poor Damn Donovan Peoples-Jones (JPDDPJ) is something we're going to have to live with, but yay palindromes.