The biggest problem, and it isn't even close, is continued poor play of the OL.
That having been said, as to the matter of running game versus passing game, I'll skip the Alex vs Frank portion of it and go to another area that is more of an issue than many seem to recognize: Receivers with speed.
Several articles are out talking about the speed of the Eagle receivers. They are fast. VERY fast. And they cause problems for everyone, and they will likely cause problems for the 49er secondary on Sunday.
In contrast, the 49er receiving corp has been focused on being sturdy blockers for a power running game rather than speedy receivers who can get open. While the Eagles were picking DeSean Jackson and Jeremy Maclin, the 49er grabbed guys like Arnaz Battle and Joshua Morgan, two guys who block well but do not scare any secondary in the league. Michael Crabtree was highly touted for his college exploits but he has only average speed for an NFL wideout. Ted Ginn has speed but due to his receiving deficiencies he is useful only as a returner. He's exciting in that role but no one fears him the way they fear Maclin and Jackson. Vernon Davis has great speed for a TE but due to the problems with the OL he spends far too much time blocking for the only guy on the team with speed anyone would worry about, which takes us back to the OL...
Oh yes, there has been Lloyd and Williams and Williams and a few other guys in the mid to lower rounds, skittery little guys who only come into play when there is a legitimate speed threat or two on the team, and that is something that has not been here since Owens left.
This team is still a team built around power running and just a coaching change, as desirable and needed as it was, cannot change the makeup of the personnel of the team. This is still Mike Nolan/Mike Singletary's team and it will take another two years of shrewd drafting to bring in the kind of speedy offensive players who can perform at a level that will allow Harbaugh to truly bring out the Bill Walsh offense.
So now back to the Alex vs Frank discussion...if you must...