I grew up in the country, so I learnt to drive well before I got my L's. Dad taught me in his old farm ute, which was a column shift 4-speed Mitsubishi L200. First time I drove an auto was just before I finished school, lol.
IMO for a city kid without the opportunity to learn to drive in a wide open paddock with nothing to hit, an auto would likely be the best choice. It's one less thing for you to have to concentrate on whilst inexperienced and dealing with city traffic.
As for my preference, it depends on the vehicle and it's intended usage. I'd hate my Navara if it was auto, 4x4s should be manual unless you plan on doing a LOT of towing IMHO. If I was building a car for combined track and street duties it'd be manual, if it was purely for the street it'd be auto. I'm lazy these days.