Josh Marshall and Andrew Sullivan make the case that one reason Hagel's nomination has become such a hot potato is because he symbolizes the Obama administration's pivot away from the Middle East. Here's how Marshall puts it:
Let’s start with what we might incompletely call the Bush/neoconservative approach. It is a belligerent unilateralism, a vision based on an abundantly powerful and yet deeply endangered America, and — very significantly — one that sees almost all the big issues and future security of the country emanating out of the zone of conflict stretching from North Africa into Pakistan. In other words, it’s about oil, Islam, the Middle East and Israel.
The people around Obama have a different take on goals, threats and tactics. It’s not just that we can’t continue — either in security or fiscal terms — with open-ended occupations of Middle Eastern countries or hapless efforts to ‘transform the region’. It’s that the Middle East is fundamentally more yesterday’s news than tomorrow’s and that we need to be in the business of making it more yesterday rather than less.
There are multiple lines of attack against Hagel, so I don't know if there's really one meta answer for why his nomination has generated such controversy. Still, Marshall makes an interesting point.