The real question then becomes: is the plan necessarily bad? To get the obvious out of the way, there will be no impact on funding for the war, if anything we'll be sinking more into the abyss that most call Afghanistan and there are no signs of a 14 month withdrawal in Iraq. So in the short term no one can say that Gates/Obama (Gaoma) plan will hurt our current operational committments. What I'm worried about are long term implications.
What's important to note about Gaoma's plan is that it shifts the operational focus of the military to COIN ops and low scale conflict operations. The programs that might get axed are not only those that Gates says are bloated or inefficient but those that are centered around large scale conventional war. Gaoma have staked their bets that the age of nation-state wars passed with last century and that the low intensity conflict is going to be the problem of the future.
A lesser analyst would focus on raising a political battle cry that this is the problem, "we're losing against China/Russia, China is the lurking enemy." These concerns are certainly true and valid, but what I'm more worried about is what this President and future Presidents will do with a military that becomes increasingly built on low scale conflicts/operations. If they think they have a military that is built to handle these problems than I feel like they'll be more willing to use it and deploy us into more conflicts. The real concern than becomes whether or not the Military will be used for our security, or the moral maxims of whatever teleprompter chained dupe the short sighted masses elect next (even worse....whatever problems the UN drags us into).
In addition, we've already seen the costs of COIN focused militaries in their confrontation with large well armed conventional forces; they get obliterated (see the latest Georgian conflict). If the conventional force has the political will to disregard concern for civilian safety than no low-intensity military can stand up to it. Sure, the age of Western Nation States using their militaries in such a fashion is over, but we've seen no sign this is true from Russia or China (thinking of the brutal repression over the last year of Tibet). With a long term change in direction we are subordinating our military initiative to them while simultaneously potentially dragging ourselves into numerous humanitarian messes across the globe.
This will be the eclipse of the American Epoch.