If you just want a toy for off roading and pack light when you camp, then a wrangler is great. One of my good friends has one - as a toy - and we go out wheeling a lot. Its great off road, but two people and a weeks worth of camping gear are hard pressed to fit. Its actually laughable. He puts a hitch rack up front and in back.
The Wrangler Unlimited actually has pretty cargo size...and since, like FJ, the seats and floor are waterproof, cargo storage becomes easier if you have dirty stuff.
Honestly I wouldnt even consider a wrangler. I know everybody claims they're capable, but I think that they're a bit undersized and flip often because of the short wheel base.
See above...Unlimited has awefully long wheelbase, which makes for very average (pickup truck like) breakover angle (20 degrees in Rubicon form). But, it does improve stability and storage capability.
Over the FJ: FJ is too small for my needs. I need to be able to put carseats in the back seat and get small children in and out of the carseats. FJ is good for a twenty-something owner with no kids, but I needed something bigger and more practical.
Over the Jeep: Jeep quality is poor. Compare the resale value of a 3 yr old Jeep against a 3 yr old Toyota. There's a reason the Toyotas hold their value. It's little things - like the adhesives that Jeep uses on the interior will go bad/dry out after a few years. If you plan to keep it, it will drive you crazy with rattles after 3-5 years.
The Wrangler resale value has traditionally been very strong, possibly on level with 4runners! No kidding...just look it up. Of course, this does not apply to the other Jeep models.
But, i agree with everyone above. Jeep Wrangler Unlimited is seriously lacking in everyday comfort. The new Wrangler (2011+) has a much improve interior, but the rear seat passengers will hate you! The rear seatback is NOT adjustable and thus, the passengers sit very upright...not comfortable for long distance for sure.
The current Wrangler is actually not as noisy as the previous generations...windnoise will always be a factor given its square shape. But, road noise itself isn't all bad, even with the BFG MudTerrains.
The biggest problem and the main reason why i will never get one is the safety aspect. Front crash scores have been good. However, it lacks side curtain airbags. There is optional front seat side airbags, but this only protects the thorax...and the rear passengers have no side protection. Upright rear seating also limits how happy my kids will be. And like most of you, i spend a lot more time on-road than off-road. So, the Wrangler is a cool 2nd car for local off-roading, but i much prefer something like the 4runner for long distance use or off-roading in another state.
As for the FJ, my brother has one. He has a 6-year old and a 10 month old. He manages fine...as the FJ is the family "minivan". The problem i have with the FJ is visibility and the fact that rear passengers feel claustrophobic because there is no real rear windows other than small portholes high up. The obvious nice thing about the FJ is that it is good off-road and has a waterproof interior.