When it comes to the shotgun... of course it's an indication that a team is likely to pass. It's a passing formation, intended to help the QB by eliminating the dropback. It's possible to run out of it but that's less than optimal. Defenses have known that a shotgun likely = a passing play since the formation was introduced.
The running plays people have been complaining about all week are the same plays on which Peterson gained 2000+ yards last season. Musgrave can vary the playcalling more but believe me, abandoning Peterson and the running game after a few ineffective carries is not what we want from an offensive coordinator. I don't disagree that there's some room for improvement in the playcalling and use of personnel but the bottom line in last Sunday's game is: for the better part of 4 quarters, the Lions defense whipped the Vikings offensive line. No offense is going to look consistent or efficient when that happens. Blocking is the engine that drives offense. Any play can work if it's executed well but screens and reverses probably aren't great calls against a defense that's stacking the box. The best way to deal with that is to go over the top of it and they did that successfully a few times.
Just to be clear, I'm not saying Musgrave doesn't deserve some criticism but it seems like a little perspective is in order. The Vikings offense outscored more than half of the league last Sunday! They can be better and they should be better but that starts at the line of scrimmage. There's not much Musgrave can call that will work if the blocking stinks.