you say you'll be limited to a second gen truck. well i've never driven an auto 1st or 2nd gen, but from what i hear, the auto really sucks power away from them. neither the 22re, nor 3vze are terribly powerful, and attaching a slushbox to it will make is worse. i don't do any crazy offroading, but i can get along just fine with my 5-speed. auto is good for slow rock crawling when you need the extra torque from the torque converter, but i think that's the only benefit, and if you have good short gears you don't need the extra torque anyway. there's only one time i'd vote for an auto over a stick: the new mercedes amg C cars (i don't think you can get a stick anyway). the auto tranny's in those cars are so smart that they shift better than i can. they're a real blast to test drive. one other time i may vote for an auto (but would probably still get the stick for the coolness factor) is in a F-350 (or dodge 3500) truck for towing. the auto trannys there were designed for towing, and do a better job than the stick, but i'd still rather be able to pick my gear when going down a hill, rather than hopeing that the electronics in the transmission will hold me in the right gear.
anyway, enough rambling, my vote is go with the stick, if you find it too hard to drive off road, add a marlin dual case (
http://www.marlincrawler.com) to it, then you'll never have any issues.