Having driven the FJC as part of the Trail Team, and having been part of the Media Drive event for the 2012 Wrangler, I've got opinions on both
The Wrangler (Rubicon) is a nicer offroad vehicle. Hard to beat solid axles, factory 4:1 t-case, factory diff locks, and a 4-door with a removable top. The new Pentastar 3.6 V6 is nice...on and off road. 60-100ish mph was pleasant for passing

Handling is okay, but not terrible...I could get the inside rear tire to lift on hard pavement cornering. Braking was good, pavement to gravel transitions were handled well. Trans felt fine to me, and we pushed it hard. It's not a sports car, don't drive it like one.
2011 was a major redesign of the Wrangler, and 2012 offered the new Pentastar motor.
2012 Jeep Wrangler – NEW Pentastar Motor Changes Everything! | RockCrawler 4x4 and Offroad Magazine
The FJC wins in the reliability department and for on-road use. Blind spots, sure, but like any vehicle you get used to them quickly. Rear seat access is for gymnasts. Handling is good with the IFS, and predictable. The FJC is an enthusiasts vehicle or one you own to be different. I know a guy on MUD with over 120k on his 2008, and has had great luck with it...work daily driver and offroader as well.
Honestly, as a primarily-offroad user, I'd prefer the Wrangler...just hard to pass up the factory features for that purpose.