Some of it is fairly obvious, but there's probably a fair amount that is nuanced and difficult to put a finger on.
1. As others have pointed out, our offense was allowed to languish far too long. Obviously, a huge culpability lies in Kirk's loyalty to Brian. But, the biggest factor was we were winning in spite of the offense. Success creates a false sense of security and can blind you to a major problem. It also gave Kirk ammunition (spoken or not) against any criticism.
2. The domino effect of #1. Those in sports living outside of the Iowa bubble made the program the butt of jokes for almost three years - not only the offensive performance itself, but the inability of those in power to acknowledge it or make an effort to rectify it. Recruits that would otherwise be very interested, even on defense, take notice and decide why would I want to go there?
3. Poor quarterback development. This goes much further back than Brian. For whatever reason, KOK always gets a pass here, but our QBs with rare exception have looked stiff and mechanical for years. I honestly cannot recall the last time I felt comfortable and confident when one of our quarterbacks dropped back to pass. It's almost like I feel relieved when the pass is completed. I believe it was Nate Stanley who made the comment that he was working with a QB coach on his mechanics because no one ever did that when he was at Iowa. Huh? Is Lester the answer here? I don't know, but every time I watch other college quarterbacks sling the ball around in rhythm I feel a little jealous and frustrated.
4. Schemes. You can see some light at the end of the offensive tunnel with Lester but it's going to take time. Defensively, Phil is a God and has had great success, but in this day and age, the "bend but don't break" cover-4 zone scheme isn't going to get us over the hump with the top tier programs. The scheme is predicated on offenses making mistakes if given enough rope. The problem is, elite offenses aren't going to make enough mistakes, They will gladly pick the zone apart with sustained drives over and over. It we want to compete with the big boys, we'll need to come up with more wrinkles.
Sorry for the long post. It's raining here today, so I can't tackle the mountain of leaves....