It's purely personal preference.
Before my 07, you couldn't get me to test drive an auto, let alone buy one. Manual or nothing for me.
Before I joined any forums though, I realized the power band of a diesel and the constant shifting of a manual would make the auto a better go-fast option, so I got the 07 auto with full intentions of having 1k hp and racing and planned on a manual rig to tow with.
Long story short, that didn't happen, and now after driving so long with the auto, you'd be real hard pressed to convince me the manual is better.
The auto is superior in daily driving, it's superior in towing, it's superior in acceleration (empty or towing, yes it matters), it's just an overall better option. My opinion.
Now, I still enjoy rowing gears, and a dedicated tow rig pre-6.7 (4 speed auto) the manual is better. But the 6 speed autos have turned the tables.
Were I to buy a new rig today, hands down it would be the Aisin.