The new 2012 have a new motor and 5 speed auto transmission that come from the grand cherokee, the manual is the same 6 speed. More power but at a higher rpm rate then the old 3.8. Just this fact may sway you into the new model. The 2011 models were refreshed with a all new interior so that is something to consider vs. the 2007-2010 models. Some like the new look some don't. If you plan on putting big tires on it axle gearing will be an issue so you might want to look up some threads on gearing. I would avoid a jeep with 3.21 axle gearing unless you plan to re-gear it in the future.
The automatic transmission in the 2007-2011 is poorly matched to the gearing in the axles and therefore the performance is rather lacking, if you can drive a manual and are not planning on building a hard core rock crawler I would recommend the 6 speed. I have not read much or driven a 2012 auto so I cant really comment on that combo.
If you are looking at older jeeps, the 2007 models had several available options that were specific to that year. You could get 4.10 gearing in any model not just the rubicon. You could also get the rubicon electronic sway bar disconnect, and a rear E locker.
A stock jeep is a very capable off road vehicle, you will be impressed with what it will do. The biggest upgrade for a stock is in the tire area going from an all weather to a mud terrain makes a huge difference in wet conditions off road.
The rubicon model will give you some upgrades that are very expensive if you have to purchase aftermarket. The front dana 44 axle and the front and rear lockers will cost close to $5000 and the 4.10 gearing with the 6 speed manual will allow you to run up to 35" tires without doing a re-gear. Re-gearing and axle can cost between $1200-2500 depending on your location. The Rubicon also comes with a super 4:1 gear reduction in the transfer case vs the 2.72:1 on the other models. This will make slow driving over obstacles and up steep slopes easier.
I hope you can find the right jeep for you and welcome to the community
If you learned something new today, you had a good day.