For what it is worth, I think that the problem with the running game is "all of the above" with AJ's absence, McKinney's injury, Flanny's play, the o-line's lack of a mean streak, and our RB stable all working together to make us the worst running team since... uh... well, in a long time.
AJ being out has hurt for the reasons that checo446 described. So said, I think that as Walter and AD continue to be productive AJ's absence will be lessened in terms of impact to the running game. Defenses have to respect AD's speed even though he's not the playmaker that AJ is. When AJ gets back, though, I can't help but think that it is going to help the run game significantly. I know its not "Moss, Stallworth, Welker" but the troika of "Johnson, Jones, Walter" or "Johnson, Davis, Jones" is actually pretty dang good and should take some of the pressure off of the run game. I hope.
I agree wholeheartedly with the school of thought that McKinney's loss was what primarily derailed our running game. Flanagan is built like a potato with toothpicks shoved in it and appears relatively soft. Now, I'm sure that he could probably tear my arms off and beat me do death with them, but I'm not a Grady Jackson sized NT, either. I have no doubt that Flanny has the brains to make the protection calls, but I do have serious doubts on his ability to kick arse in the trenches. It's the old Matthew 26:41 verse in action: "The spirit is willing, but the body is weak."
I was optimistic with regards to seeing Studdard and White in the mix this week but my hopes got deflated when I read Kubiak's statement that he's rolling out the same old stuff for the Tight 'Uns. I've said before (and I'll stand by that statement) that the O-line just doesn't play with a mean streak. Studdard seems to have it based on some of his quotes (can't recall seeing him play) and I don't know squat about White. I do hope, though, that maybe one or both of these young men is as mean as a rattlesnake and can bring some "I'm-going-to-punch-you-in-the-mouth-all-day" attitude to that o-line. I think they need it badly.
I trust Kubiak and Sherman (to an extent) but seeing us get stuffed so many times on 3rd and 1 and unable to come up with a yard makes me think that they need to be working on something a little different. I don't know if that is a shift in playcalling. A shift in personnel. Putting icy hot in jockstraps. I don't know what it is but I'm hoping they'll do something. At work, if we're doing something and its not working, we fall back, regroup and come at it from a different angle. We operate on the mantra of "Insanity is defined as doing the same thing over and over and expecting the outcome to change." That's what I'm consistently seeing since McKinney left. We can't run in the past three weeks and yet we continue to do the same things. I know I'm just a fan and maybe my expectation to see some kind of change is unrealistic. But we're already about 40% of the way through the season and things aren't improving.
Finally, we all know that Ahman was not our running back of the future and that he's a stopgap. He's the only RB that we've had that has shown any kind of RB1 ability and he's also been on the field precious little. Our RB2 and RB3 are non-factors for the most part and can't seem to make anything happen behind that o-line. I know Hunger Pain Dayne did some solid work for us last year against the Colts, but he's been nothing but frustrating to watch this year. Same thing with Samkon. He looked rusty against the Colts and hasn't looked better since then.
In short, I think that we've got so many different things working against our run game that we may not be able to overcome them this season. I'm not saying that the season is lost, but if we continue to play with the same starters, same lame-arse hybrid blocking scheme, and mediocre RB play, we're probably not going to run the ball for more than 60-70 yards a game. That, in turn, is going to let folks key on our WR's, hunt for Schaub's head, and leave our defense on the field for a looooong time every game. It's a bad recipe, and one that I'm hoping that Chef Kubiak will start changing soon.
Just my $0.02 (and that's probably about what its worth)