I've done both, pretty sure of that.
Don't call me a bad-ass just yet, because I've been wandering around trying to figure out which is best too.
Last couple of times I worked on the car, the trans was in and out, or the head was coming off.
Pulling the motor with the transmission, is by far the best way to do this.
Being that the best way to pull everything is from the bottom (just like the factory would install it in reverse order), the complete assembly with the north south bar in place would come down
with the car poised above it.
To however, remove the motor with the car sitting at a reasonable height and for most home repair situations you will need the following.
A load leveller, likely available from Harbor Freight or the like, in my case here in Canada, Princess Auto.
See part here:
http://www.princessauto.com/pal/en/Repa ... /1580009.p
So, remove your axles, wiring, fuel, vacuum hoses and mounts (etc, etc.), tilt to a near 45 degree angle and pull.
This should be considered just like taking out an inline drivetrain, ala RWD motor and trans attached to one another, and just being able to clear the rad support/grille.
Should be easier with the 4 cylinder.
Best to drain the oils first.