I'm beginning to think that the lack of difference between the party policies isn't that they're the same party...I think the institutional attitudes of various agencies doesn't change with government rotation because most of the employees of the agencies don't change. That can be as good (if the party you disagree with is in power, it's hard for them to gut an agency they don't like), and it can be bad (an out of control agency can almost do whatever the hell they like, since they know they can outwait any mangement they disagree with).
I'm not sure how to solve this one, though...if you clean out the entire upper echelon of an agency at administration rollover, then you risk seriously politicising even the most bland agencies. On the other hand, some of these agencies clearly need an attitude adjustment, and I really do think the attitude problem is endemic to the entire culture of the agency, not just their leadership.
Maybe a max term for any federal employee that they can't work for any one agency for more than 10 years?