alot of the jkers use auto. its easier for climbing. in fact 90% of the JK jeeps that climb in Utah are autos.
as for me, i went with a manual TJ and i am never going back to automatic. its so much more fun and interactive IMHO.
but the JKs are capable of doing some "jeep" things =
depends what your gonna doing. and if you want that rugged feel of a jeep or the luxury of heated seats, leather, blah blah blah.
and sure one could argue those are heavily modified JKs , but what the hell, half of the TJs running are heavily modified aswell.
as for advantages? manual =more fun, better MPG, more control over rpms while on and offroad, less moving parts, and generally easier to fix.
Automatic= Easier ?