You asked what Hagel disagrees with the Bush Administration on...the answer - Pretty much everything - this is an excerpt of what Hagel said:

"As to my personal opinion, which I have not been shy about sharing, I think as most of you know in speeches or interviews, this administration in my opinion has been as unprepared as any administration I'm aware of, not only the ones that I have been somehow connected to and that's been every administration -- either I've been in Washington or worked within an administration or Congress or some way dealing with them since the first Nixon administration.  I would rate this one the lowest in capacity, in capability, in policy, in consensus -- almost every area, I would give it the lowest grade.

And I have to say -- this is my opinion -- it is my opinion that this is one of the most arrogant, incompetent administrations I've ever seen personally or ever read about.  (Laughter.)  And when you think of the time and the opportunities that have been squandered by this administration, that's how you judge -- you all know about this, especially those of you in financial services, but anybody who does anything with time."

Here are a series of awesome links (the first one has the quotes and much more on policy issues as well):

http://www.cfr.org/...

This article shows that Hagel is a pragmatist at heart (just like Obama).  He does not believe in the Bush Administration's worldview when it comes to Iraq, Iran, diplomacy (he believes in talking with your enemies just like Obama does), global warming - he believes there are issues with our environment (but they have to be solved in conjunction with business), and we need renewable energy sources and conservation.

Hagel says, "And so I -- to your question about who is in my opinion closest to my foreign policy, John McCain is the only one that I -- of the candidates that I've worked closely with -- of the Republicans.  Now, Joe Biden -- I'm very close to Joe Biden's philosophy about foreign policy.  I suppose of all the candidates out there, including McCain, I'm probably closer to Joe Biden's.  And I think Biden would be a very good president.  I think Joe Biden would be a very good secretary of State."

He also says:

"What has prevented a World War III or a nuclear holocaust, in my opinion, more than any one thing, is what Truman, Eisenhower and Marshall and others worked for after World War II -- building coalitions of common interest -- the United Nations, NATO, World Bank, IMF, dozens of multilateral banks and institutions.  Why?  Because they were focused on a common interest.  This was not a zero-sum game.  Alliances are absolutely critical.  And what we learned from Iraq is that you can't unilaterally, arbitrarily march into a country, invade a sovereign nation, regardless of the dynamics or the reasons or whatever you want to make as the primary focus on this, without alliances, the strength of those alliances."

http://swamppolitics.com/...

http://www.huffingtonpost.com/...

And this is interesting...he basically says that both Rudy Giuliani and Hillary Clinton are reckless on their Iran stance (and that was before Hillary's "obliterate Iran" comments, but Hagel seems to be a good judge of character):

"The politician who has spoken the strongest words against the recklessness of Giuliani is not a Democrat, but Senator Chuck Hagel of Nebraska. It was Hagel who had the nerve to denounce the self-indulgence of Giuliani, when the latter pushed hard to outbid the president in rhetorical posturing against Iran. This was speaking of war in such a way as to make a war inevitable, said Hagel; and it put our own soldiers at risk. Hagel rightly included Hillary Clinton in his condemnation. For her vote to declare the Islamic Revolutionary Guard a terrorist organization, and her scorn of the "naivete" of talking to Iran, added up to another attempt to overmatch the president in the game of who is the toughest.

One other thing sets Hagel apart from Clinton and Giuliani, as it also sets him apart from Cheney and Bush. He has fought in a war, a war on the ground, and has seen what it is for soldiers and civilians to die."

Hope this helps!  Let me know your thoughts.