The Obama administration announced that Khalid Sheikh Mohammed and two other detainees from Gitmo would be heading to NYC for a trial by jury. There were three other options, continue having them remain in Gitmo indefinitely, having a civilian trial without a jury, or having a military commission.
The disadvantage to remaining in Gitmo is sort of obvious, that Obama said he would close Guantanamo within a year. The administration thus had to begin doing something with the prisoners quickly.
Having a trial without a jury was problematic, since a judge under so much scrutiny from the media and groups like the ACLU might have a difficult time arriving at a guilty verdict.
The case against a military tribunal is less clear. The advantage to this scenario, which has been employed a number of times since 9/11, is that the standards which are employed against citizens at a trial are less rigorous. A decision was also announced that five others being held at Gitmo would be tried using this system.
It appears that, for the three scheduled to be tried in NYC, the evidence that they had a part in the actual 9/11 terrorist attack is so overwhelming that a jury would convict, and that no Appeals Court would ever countermand that decision, based on violation of rights standards.