If you want my honest to god opinion of what the problem is...
Well.. Everything. Something is clearly off with Joe, and it's mental. The scheme... Well to put it frankly it sucks. Even if Pitta exaggerated his claim(I personally think Harbaugh is being a politician again and is just trying to cover his ass. Again, put yourself in his position, you'd probably say the same thing. Not that I think what Pitta said is totally true, but even going back to last year.. There is tangible evidence to back up his claim. Particularly with how we use the TEs. Pitta would know, he was in Watson's position last year).
Flacco isn't to absolve from blame either. He's certainly part of the problem. He has the power to audible out of plays that Marty calls. But he's also the one he can fix. He still displays certain traits of a franchise QB. Something is clearly off with him mentally, some sort of discomfort. He used to have good mechanics until last season tbh. That's a mental problem, and I don't know why he has it, but he does. It's fixable, but we need the right coach to do it(hence my massive advocation for Kubiak. We're stuck with Joe anyway. Let's bring in the one guy who has had consistent success with him).
Sure, we have invested a lot of money in the offseason, but some of the investments have been poor. The TE corps is either injured, or suspended at all times, Maclin is the only WR who consistently produces and has completely sound hands, Perriman has regressed somehow from last season, Buck Allen is more of a reciever than a running back, and.. Well Alex Collins is pretty good.
I do think us losing Danny Woodhead for ahwile has hurt the team more than anticipated. On those checkdowns he's shifty and quick and would be able to garner more yards. He has a few years left in the tank and his return will likely help the offense greatly.
Sure, the offensive line is playing well... But how long can they keep this up without Yanda there? Furthermore, what happens when they play a defense that is legit? Investments are still going to be needed there. No question. I still think we should go offensive line in the first few rounds.
The supporting cast has some questions. I'd honestly keep Maclin, Collins, Dixon, Woodhead, and Watson on a one year deal that's dirt cheap going into next season. This is the offseason to invest heavily with the weapons. Get a WR or two in FA, draft a WR, TE, or maybe even a RB even with the success of Collins. Collins keeps it up, he's going to be a #1 back. I think Marty is a problem, but not necessarily entirely as a playcaller. Flacco is not a fit in this type of offense. Which I think is a MASSIVE problem here. Sure, Marty isn't a fantastic playcaller, but let's not act like he's 100% to blame. I think that Pitta's claim has some validity, but either way Flacco is not a pure WCO QB.
Honestly though.. Marty and Harbaugh need to go. While Flacco is a part of the problem they have made some porous decisions that have ultimately made his life harder imo. Flacco is a SB winning QB who used to play really well in big games. He had proved that he was a franchise QB, and while it is a shame that it is almost time to find his replacement, I still don't think he's done just yet.
I still think getting Kubiak out of retirement is the way to go. We're stuck with Flacco's contract for awhile.. MAXIMIZE IT. GET YOUR MONEY'S WORTH. Our olinmen have had success in the ZBS before and would likely do so again. Put Flacco in an offense that plays to his strengths. Make him more comfortable. Worst comes to worst, we can draft his replacement in 2019. This offseason needs to be about the supporting cast on offense and offensive line and building a new scheme. If not for Flacco, then for the new guy in the future. We have invested enough on the defense that they're gonna be set for the next half decade. Half of the rebuilding process is already done.
2018: Get WRS, olinemen, a TE, and maybe another RB.
2019: QB, safety.
That's the play... 2018 will be a last push/chance for Flacco to redeem himself, likely under a new coaching staff. If he fails, then so will the rest of the team. it's younger than we are used to and will likely have growing pains, so if Flacco sucks again in 2018 we should have a top 15 pick. In trading range for a potential QB. And 2019 does not have a bad QB class.