Hi

Have not stayed at the Marriott ( I'm a hilton person) but from the excellent reviews above I would say that

Standard rooms look larger at the Marriott than the hilton
Rooms have balconies at Marriott and probably better views than the hilton which has no balconies
Suites at Marriott look better than at the hilton ( have not stayed in a suite at the hilton)
Hilton has a shallow hot bath which was quiet good.
Afternoon offerings in the Hilton Executive lounge was very good
Marriott closer to the Nagasaki tram stop and slightly closer to the JR station gates than the hilton which is just across the road at the opposite entrance to the JR station

Regards

TBS