49ers penalties 2012: Timeouts and delay of game

ESPN's Mike Sando tweeted an interesting statistic earlier today, pointing out that Alex Smith is tied with Tim Tebow for most delay of game penalties since the start of the 2011 season. Although a given delay of game can be blamed on a variety of people, the quarterback is the one called for the penalty.

Over the last season and a half, one of the concerns I think most of us have is the 49ers use of timeouts. It seems like more often than not, the 49ers have burned all three first half timeouts with most of the second quarter still to be played. Against the Arizona Cardinals they did save a timeout for the final two minutes, but they had to use a pair of their timeouts because time was running down before they could run their plays.

Unfortunately we have no way to know whether this is slow play-calling from upstairs, or delays on the part of Alex Smith. The offensive coordinator calls in two plays to the quarterback, giving Alex Smith the option to run the play given, or "kill, kill kill" it and make a change. Is it possible that is slowing things down? I don't know the specific names of plays, so I don't know if play-call length is an issue.

Whatever the case, this has developed into a fairly noticeable issue. Ideally they would use the bye week to rectify it, but if the length of play-calls is part of the problem, then I'm not sure there is really an in-season fix at this point. Any thoughts on this issue? This seems to be the biggest weakness for the Jim Harbaugh offensive coaching staff.