First, I wouldn't get too hung up on the debate between six gear ratios versus five. I tend to think all the hype about six and now even seven speed transmissions is just a silly marketing ploy. There is nothing wrong with a gearbox having five well-placed ratios. In fact, some times it is preferable to do less shifting.
Anyway, my '06 is an auto. One benefit to going automatic is you get a better tow package option. The automatic with tow package includes an external tranny fluid cooler, not just built into the radiator but an actual core completely seperate from the main radiator. All this allows a higher towing capacity than you can get with the manual, if that matters to you.
The auto is a shifty beast. It will shift around quite a bit in traffic but is pretty easy to control with your right foot. It also downshifts for you on steep grades, which is sort of cool. Conveniently, you can set it to whatever highest gear you want, as the shift lever has positions for each gear between 1 and 5. If it hunts too much for your taste, you can make 4th the maximum gear. Same with any other gear.
There's no clutch start cancel, so you can fire up the truck without having to get in to push the brake and clutch. Handy, but hardly a deal-breaker if you think you want the manual.
That's my $1.50.