He was a better coach by the time he left, but as a previous poster said, it was too late at that point - things had already spiraled too far.
The big issues for me:
Lack of player development (it's hard to name a single player under Alford that was a significantly improved player at the end of their career than they were as Fr)
Lack of player retention (this is multi-faceted - good players that transferred, boneheads that got into trouble that should have never been recruited in the first place, guys that really didn't want to be here...or got here and realized they didn't want to be here)
The game day coaching itself did show some degree of progress as Alford went along in his career, but nowhere near to the degree where it was enough to overcome the previous 2 issues.
He had a really cocky persona, which I think caused 9/10's of his problems w/Iowa fans (and probably players too, for that matter!). Personally, it never really bothered me - a coach that gets results for my team can be as cocky as they want to be. If Alford was leading us to 20+ wins every year, everyone would have called it "swagger". Just like Drew Tate - Drew was the exact same guy through his entire career, even though if you talk to a lot of Iowa fans, you would think he morphed into some horrible monster between the end of 04 and the end of 06...the W's & L's are what dictated perception.