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There was nowhere to send the prisoners. US states wouldn't take them, and freeing them wasn't an option.
https://www.pbs.org/newshour/show/obama-failed-close-guantanamo
I remember this being the big reason. The US didn't want to let them go, and no state wanted to take them.
Expending the political capital necessary to push it through would have consumed his presidency in the process. It was a matter of priorities within the political reality of the era.
Or, more succinctly, it was inconvenient.
Also, imperialism.
Congress wouldn't let him, iirc