I prefer the auto hubs on my GF Nissan Xterra. It's 99%+ of the time on-road, and when she goes off road, it's almost always fire roads. We've taken it out in sand & rocks out at King Of The Hammers a few months ago. They performed just fine, and it was nice not having to get in / out of the vehicle every time we wanted to use 4WD (both the Xterra and Tracker will shift between 2 & 4WD hi-range on the fly). In crazy-bad weather I've shifted (on the fly) into 4WD for stability (and shifted out to make sharp turns). Given the weather conditions - it was nice to be able to stay in the cab & shift in / out of 4WD while driving (yes, I could shift in / out of 4WD in the tracker too, but I'd have to get out at least once in mercyless rain / wind to get the hubs locked in).
For heavier trails, I like the manual hubs. In crazy rock gardens, or more technical trails, it's important to have 100% predictability. It's also bad to allow the drivetrain to gain momentum before something "locks up" and creates a shock load... even if for only a partial rotation.
Either way - the hubs themselves rarely come into consideration for me when buying. There's far more important things to me when buying (condition, engine size / type, transmission type, air conditioning etc), and the hubs are easy to swap out.