The main culprit is their cap money situation. Some moves they have made the past year or 2 may have been in anticipation of not being able to re-do Joe's deal to be more cap-friendly (if it does get redone there's always a chance it still won't be "friendly" enough).
Nonetheless, take a look at some of these numbers. They currently have $21,913,933 tied up in dead cap from player cuts or trades (some of whom are cut, brought back, and cut again, and may even be brought back again! Canty and Asa are great examples of this). Rice, Ngata, Jacoby and Canty add up to $20,291,667 of that money. In addition, they have $15,489,045 tied up in players on IR, IRDTR, and PUP, and $13,880,212 of that is going towards players that were expected to be large or major contributors (Suggs, Elam, Will Davis, Urban, Taliaferro, Campanaro, and Pitta). In total you have $37,402,978, nearly 26% of their total allotted cap space, tied up in players that aren't playing for this team right now or are playing but are being compensated for previous cuts from the team. That's insane. Hopefully that's all this year is, the result of so much dead money and little room to go and get talent. Next year Rice, Ngata and Jacoby are off the books and that's gonna be a huge help.
You can look these numbers up on Spotrac.com.
Is leadership an issue? Definitely. Joe and these other guys don't have to rah-rah guys doing the crazy chants pre-game and all that kind of stuff. But him and the other guys that are supposed to be leaders do need to communicate with guys on the sidelines between drives, gather them around, talk, plan, get in their face, whatever, and light a fire under all their asses. They do need someone to rally around. Joe, SSS, Forsett, the O-line the D-line, and J. Smith are the only one's who seem to play like they care right now. They need to wake everyone else up somehow.
But ultimately leadership can only get you so far. And as long as the cap situation is this bad, it might not matter how much leadership there is when you have no money to shore up the pitiful depth (if you can even say there is depth) on this team. Hopefully next year they have a better game plan.
Also, can someone please tell Trestman that on the occasions where they come out throwing and Joe's completing 1 pass after and getting in rhythm, don't take the ball out of his hands. Keep the foot on the gas in that situation. As long as he's passing well there's no reason to get cute. These past 2 games they came out looking pretty good and then they seem to take it out of Joe's hands at weird times when it seems like they shouldn't have. I don't want Joe throwing more than like 35 times a game, but if it's working, he's the only guy capable of carrying this team right now, don't take the ball out of his hands!