I've never done it on a JZ motor, but I have read alot about it, here is what I know from research:
Your power band will be vastly different with less power and torque below the boost threshold (where you start to make positive pressure in the intake). IIRC, the 1JZ stock twins don't have a mentionable point where they make boost, they simply always do, even from idle. So you'll give that up, plain and simple. It'll be like driving a 7M car with a CT26, only more gutless and actually pulls to redline... ok, so it'll be nothing like a 7M, nevermind, lol.
Long story short, your power will all move up higher in the RPM band.
In terms of reliability, it should theoretically improve if the turbo is installed with high quality components and good hoses, couplers, ect. The stock CT12 (A's?) are notorious for failing... mostly because they are comprised of archiac turbo technology.