Having gone to multiple games for both teams, and trying to be completely objective, I'd go with the following:
QB - Iowa State, slight edge
RB - Iowa State, pretty big advantage
OL - Iowa State, slight edge
WR/T - With Decker out, pretty even, maybe ISU very slight edge (With Decker, it would be big Minny advantage)
DL -Minnesota advantage
LBS -Minnesota slight edge (better athletes)
DB - Even
Kicking - Minnesota advantage (ISU has had mulitple blocked FG's & Extra Points)
Punting - I'd guess Iowa State slight edge (but don't remember anyting about Minny Punter)
Rest of Special Teams - Even
Overall Talent - Minnesota advantage
Coaching - Iowa State advantage
Again - Not basing this on any stats, etc. These are just my thoughts based on having seen (in person) both teams play multiple games.