The MAIN drawback to Kicks is the aluminum front IFS. Get the GV steel stuff, or you will likely break.. especially with a welded front. In my opinion, if you are going to weld the front, I would invest in a two wheel LOW kit, I think they are a little over $100 and allow you to use low range in 2wd, that way you could leave the front disconnected unless you really needed it.
The transfer case bolts to the back of the tranny on kicks, so yes, they do have gears for the autos..
and YES the autos seem to be better for offroading.. I wish I had one.
You don't need a lot of lift on a kick to get where others go with more lift. Remember, I only have 2" in a BDS suspension package.. with a great deal of trimming, I am running 31's just fine.
Instead of putting on a body lift (YUK!) I trimmed the rockers off, and put the sliders up where they would be on a body lifted Kick.  I have the same ground clearance of ANY other kick on 31's. It just doesn't look like it. I have less break over than a lifted sammy, but I am WAY WAY WAY more stable.. That I guarantee.
Check this picture. I barely drug at "V rock" at the 909 trails. I climbed stuff others couldn't, and didn't spin where Sammy's spun...

Tires and low pressure contribute a great deal... but a stock street tired, un lifted, un locked Tracker went almost EVERYWHERE everyone else went... It was funny as hell...