Ok, like many others looking to decide between two vehicles, both 2012 models and automatics. Driven both and in the end doubt there is a 'bad' choice. I am not a rock crawler, but a hiker in the NW who goes mostly on logging roads and the occasional deactivated road to get to trailheads. Also my DD, but most weekends out to mountains.
Pros for the jeep: will more than meet my needs, simple but very functional. best off road given locking diffs, electirc sway bar disconnect and great ground clearance/departure and approach angles (tend to be a lot of water-bars/ditches here). lots of solid armour underneath. Cons: a bit rough to drive, but hey it is a jeep and the roof comes off if you want it too. reliability is mixed, though of late it looks much better. Exped Portal rates highly however. Note that breakover angle is only 20.8 on the Unlimited Rubicon.
Pros for,Toyota: locking rear diff and ATRAC as well as KDSS are a close match for jeep off road. With a good driver they have taken almost stock model (except tires) on the Rubicon trail to test. it is a Toyota - reliability in spades. This is in fact a Land Cruiser in a Prada form. good road manners (much more car like though dull) but also,good off road. ExPed Portal gives as a runner up,to Rubicon. Cons: poor tires, will need to replace right away.Approach angles Ok at 33, but departure low at 26. much less than a rubi unlimited though the breakover angle is better at 24.
Bottom line: Rubi probably can be had to about $2k or $3k less. my biggest concern is relability as used to good vehicles and also no worries off road. My wife likes the Toyota largely for reliability. Maybe Scott Brady will chime in, but pleased to hear others views/thoughts.