The primary role of the Pentagon is to envision what warfare of the future looks like. They take a 20 year view and ask the following questions (and run the following scenarios):
1) Who is/could be the enemy?
2) What does the battlefield look like (jungle, desert, urban, etc).
3) What kind of weapons/tactics will be used against us.
4) Most importantly, what type of military hardware would we need to have in order to counter that threat 20 years out.
They then take this 'long view' and use that as a road-map to invest in future weapons technologies. Mind you; this road-map gets updated every year. Then again, every year, the Department of Defense (DoD) retires 5% of old military technology, and buys up 5% of what's new... and at the end of that 20 year cycle, you have a 100% refreshed military that his hopefully ready/capable to counter whatever threat is coming at us today.
When the Soviet Union collapsed in the 90's, the war plans changed to a dual-theater conflict between 2 large nation-states (i.e. Russia & China). That is the military they built up to fight, essentially a land war in East Asia. When 9/11 happened, DoD was caught *completely* off guard. The reactionary spending that took place cost hundreds of billions more than it should have to up-armor Humvee's and build MRAP's simply because they had failed to plan for battle in the mountains of Afghanistan/Iraq engaged in guerrilla warfare. (Perhaps this is why it was time to retire Yoda?)
If you shut the think tank, the Pentagon will no longer be the R&D arm of the DoD, and within 10 years, certainly within 20 we will be a completely reactionary military force. From there, I do not see how we could or would remain a military super power. I'm not stating this in order to take a position on this being good or bad; I just wanted to put it out there that this would be the consequence of eliminating this central, core component of the Pentagon - and the role it plays in our entire national defense establishment.