Only the V6 models have the 6-speed Automatic, which debuted for 2005. 4 cylinder 2006 Mazda6's have a 5-speed.
That said, the manual is really needed to experience the true demeanor of the car. If you haul things, but don't want a wagon, the 5-door is a great blend of sport and utility.
If you will regularly carry clients in the back seat, however, the extra head room of the sedan and wagon would be beneficial to you.
2004 V6 5-door MTX owner here. Just under 30,000 miles.
I think trim and such really is up to you and what you want out of a car. Keep in mind the 2006 is MUCH plainer than older years, so the Sport package is almost essential (it doesn't even look sporty).
