So very many things go into a season, but I'll take a stab and see if I can't be a little less one-sided than some (seriously, y'all will take your base argument and apply it to any old thing, it seems).
1.
One very messy off-season.
PLEASE NOTE: It doesn't matter whose 'fault' it was - the point is simply that there was so very much to pull the team's focus from preparing for the season. I do think this took a toll.
How's it being addressed? How do you address such a thing? It'll be a little better this year, but it will take time.
2.
New QB. He's good, but he's young. Only the willfully blind would ignore that there was a drop off in terms of experience, and that drop off did affect how things went in games. To what extent I wouldn't presume to know, but I'm sure it affected McCarthy's coaching, and I would bet that some reads/check-downs/play changes at the line didn't occur as they would have w/ Favre. A subtle change, but one I'm sure was reflected in play on the field.
How's it being addressed? Experience. The more he plays the more he'll learn, and those subtle improvements will occur. And the more he gets that experience, the more likely it will be that McCarthy will adjust back to a more aggressive approach (or, as may well be the case, Aaron will learn when to change that run play to a skinny post or something like that).
3.
Thompson and co. over-estimating their roster. I will say that I don't necessarily have the facts to back this one up; it's more of a gut feeling, based on the assumption that they must have thought Harrell was going to step up and therefore Williams was expendable. Now, Williams definitely wanted more than he was worth, but I do wonder if Ted would have paid that had he had a more realistic sense of where Harrell was at. In any regard, with a couple injuries a strength turned into a liability, and you don't want your liabilities to be along your front lines - thus begins a domino affect, one that we all witnessed.
How's it being addressed? Raji. Whether he fulfills his promise remains to be seen, but he was touted as THE DT in this draft, and they got him. IF Harrell can be healthy enough to be a part of the DL rotation, we're looking at that becoming a strength again.
4.
Luck/Injuries. Yeah, yeah. "No excuse!" I love that one - like a bunch of pasty wanks on the internet all become Lombardi or something. Let me be clear, here: It is not up to me to make excuses for the Green Bay Packers - I'm just a fan of the team. I'm not making any excuses, but you tell me how good our D was supposed to be when it was missing KEY pieces from last year, to wit: Cullen Jenkins, Atari Bigby, Nick Barnett. That's taking our most crucial D-lineman, our starting MLB and our starting SS out of the game. No team has the depth required to plug that many holes, not to mention holes that size - sorry, they don't. Additionally, we had injuries to our O-line, our QB (he gutted it out, but he was clearly affected for at least a couple games), our starting halfback, and a receiver who was just becoming an important piece in the offense. That's a LOT of injuries, folks, and it's not like they affected marginal players.
How's it being addressed? We have a new Strength and Conditioning staff. That's really the most you can do, other than hope you won't get hit by lightning 2 years running. Luckily, the odds are in our favor.
All the above is my own opinion, obviously. But I do see reasons for some optimism, even if I think more could be done in terms of personnel.