From my vantage point, Kyle Williams is not the problem. Not to say he never gets beat, but he's certainly not the biggest cause for lapses in the running game.
On most plays, Kyle Williams is responsible for one of the "A" Gaps (between the center and the guard). Probably 99 percent of the time, he's the first guy off the ball and filling that gap. Many times he is also facing a double team.
The majority of big runs against us are through one of the "B" Gaps (between the guard and tackle) - usually be handled by an ILB or SS ... or an outside run where one of our players fails to keep contain - usually a DE or OLB. I haven't noticed too many big runs right up the gut.
In my opinion, our run defense is significantly better than last season - even if it doesn't show on all of the stat sheets yet. I think a lot of that improvement is due to Kiko Alonso being a massive upgrade over Kelvin Sheppard at MLB. He's quick and always around the ball. Still, I've seen Alonso caught over-pursuing and out of position quite a few times. As he gets experience, I think the big runs will come less and less often.
I also think it would be smart to find an upgrade over Arthur Moats/Nigel Bradham in the offseason.