The biggest plus to the NA-T method is that you already have the engine, and spare ones can be found for a few hundred dollars. There are plenty of ways to go about the NA-T conversion ranging from piecing together your own kit, or buying an off-the-shelf kit.
The non-vvti 2JZGE motor with a thicker headgasket to lower the compression ratio can easily handle 700+ rwhp. The bottom end is near identical to the the 2JZGTE motor with a few minor differences.
For a few thousand dollars, you can piece together your own single turbo kit and choosing your favorite components
The installation of a turbo kit on the 2JZGE is straight forward and can be done in a few days.

The 2JZGE has a distributor that can get in the way with larger turbos. Some of the turbo manifolds are worse than others, but most of them can be rewelded to clear the distributor.
Lets face it, the NA intake manifold is ugly. it site on top of the engine and will hide that sexy turbo you just spend thousands of dollars on. There are some TT style manifolds surfacing however which can greatly improve the looks of your engine bay.
The stock compression is 10:1 which limits the amount of boost you can run. The safe limit is 7-8psi, but a thicker headgasket will drop the ratio to a more boost friendly level.
The stock fuel is limited by the 330cc injectors, however u can install 440cc injectors and upgrade to a LS400 MAF relatively cheaply.

A 1JZGTE swap will deliver a smooth powerband with the stock twin turbos.
The 7500rpm redline gives you broader power band.
The MAP based speed density system allows for easier and more accurate tuning.
1JZ motors are much cheaper than the 2JZGTE.

The 1JZ motor is harder to find replacement parts for.
The motor must be imported, so there may be uncertainty regarding the condition.
Aftermarket parts can be hard to find.
The 1JZ is a 2.5L engine versus the 2jZ 3 liters.
This is ont a direct plug and play swap. There is a lot of wiring involvd.
Becuase its a swap youre going to run into a lot more problems you didn't expect.

A 2JZGTE swap will deliver a smooth powerband with the stock twin turbos.
There are oil squirters on the pistons. This isn't really that big of a deal though and no NA-T people have ever complained about lack of oil squirters.
The 2JZGTE swap will leave you with a sweet 8.5:1 compression.
There is a huge performance upgrade market for this engine.
There is no distributor on this motor. The coils are ont the spark plugs leaving you with a cleaner looking engine bay.

The engine is MUCH more expensive and for the extras you get, not necessarily worth it. You can fully turbo a GE for the amount you would spend to swap a GTE without upgrades.
There are a lots of modication needed to the wiring harness when being put into an SC300.