I see your point...and I'd stipulate the only reason it seems like the Republicans are responsible is because they happen to be running things now. I recall most of the same sh-- during Clinton's reign, and I'm sure it'll go on well past Bush's. It's just non-partisan pork politics...your average senator or congressman isn't responsible for the troops, he's responsible for his state or district, so he's going to favor dumping a billion dollars into a project that gets manufactured in his state over a couple hundred million to increase soldier's health and retention rates.
And it is, for the most part, a congressional issue. I read about some bloated program or another (DD(X), LCS, JSF, FCS) every other week in Defense News and cringe. Congress is actually forcing the Navy to buy ships the Navy doesn't want, to keep shipyards working.