I have done it both ways and I think there are pros and cons for each way. It depends on what you have at your disposal in terms of equipment, work area, etc. That said, I don't think I would pull the engine just to swap a tranny, though it is true that it's easier to detach and reattach tranny and engine when they're out of the car altogether. But it's really not so bad. I was pleasantly surprised after reading all the warnings.

Just make sure your torque converter is seated on the tranny oil pump when you re-install or there can be trouble.

Good luck,
Ken