Obama's Plan for GITMO Detainees

I just read the article announcing Obama's plan on detainees held at Guantanamo Bay, Cuba (GITMO). I have mixed feelings about this, but until I read about more details I have a rather positive overall view so far. From what I understand Obama plans on releasing some people at GIMTO (problem the Uighers). Another group he will criminally prosecute in U.S. civilian courts. And here is what the article has said about the third group:

A third group of detainees — the ones whose cases are most entangled in highly classified information — might have to go before a new court designed especially to handle sensitive national security cases, according to advisers and Democrats involved in the talks. Advisers participating directly in the planning spoke on condition of anonymity because the plans aren't final.

I for one might have problems with Obama's plan for the thrid group of detainnes. Will U.S. citizens be tired in this new court as well? What are the due process rights for these individuals? Also, a new court implies that the U.S. civilian courts can't handle classified information. What about the pentagon papers in New York Times v. U.S.? Didn't civilian courts review that case? Not sure why Obama thinks it is necessary to establish a court for one group of detainees but use the civilian courts for another.