I’d also add that Pete himself said “we wanted to take them with deep shots” and everyone is blaming Waldron for throwing deep. This tells us two things, Pete is involved in the game plan and he wanted to do what everyone claiming is a Waldron thing. We’ve always played that way under Pete.
@Fade is right, this stuff isn’t that hard to figure out why it’s happening
I don't especially disagree with wanting to hit them with deep shots. We
would need to beat the 49ers on explosives, and that's the likeliest place to get them with the 49ers being down a star safety and not being world-beaters on the backend otherwise. While I would like to see emphasis short passing concepts to alleviate efficiency problems, my bigger issue is that our concepts aren't getting open at all on too frequent of a basis.
Based on my limited film and XO expertise, I think we need to find a way to have Metcalf draw more coverage as a decoy and, from there, get some synergistic route combinations going to open JSN and Lockett in space. This'll be hard without a consistent run threat. There's nothing to build on as an offense right now if we cannot find a single successful aspect of the offense to buy into, and then expand from. My thought process on a problem solving level continues, via all roads, to lead to increasing the rushing frequency, going heavy PA on most non-rushing downs, and dialing up intermediate and deep shots in between. I'd also like to see more under center looks, but that may not be Geno's forte. Pistol rushing may be an avenue to explore.
This may all lead back to a lack of detail on offense. It's been stated by a lot of film guys that the OL has fairly extreme tells regarding run/pass, which is troubling. We may be getting blanked in general, especially by man D, because the offense simply isn't detail oriented or expansive enough in scope to belay prediction by the defense.
Most of the issues I see go toward the detailed aspects of offensive coaching rather than overall philosophical issues. That'd be on the offensive staff.