Well, the choice comes down to you and what you intend to use the car for.
The LSx drivetrain is truly amazing and hasn't reached it's potential yet. .
The 2JZGTE has a proven recipe for power. it has been duplicated over and over.
If you want gas mileage, then the LSx T56 combo would net you better mileage than I see with my 2JZ, even with my 3:36 rear end, as the TH400 is only a 3 speed (no OD).
Either way, you'll ahve a potentride. If you choose to go the 2JZGTE route, just remember, the drivetrain is the inexpensive part. The expensive part comes with all of the add-ons (intercooler, turbo, engine management, injectors, fuel system, BRAKES, suspension, yadda, yadda, yadda)
Just my .02
Mike