You have a strange idea of what "a mess" means. They have only won fewer than 8 games 3 times (7 wins) in like 30 years. They finished in the top 5 for 14 years straight. While 2001-2009 wasn't absolutely incredible, 7, 8, 9, and 10 win seasons are far from the program being a complete mess. They're in the top 10 best teams of the BCS era, top 10 powerhouse teams, etc.
I just don't think you're really "a mess" when even in your worst 9 years you finish in the top 15 three times and the top 25 six times. They've always been a great program, just "suffered" a little in Bowden's last few years, and they were still winning seasons.