Cost
The destination charge is a standard charge for transporting the vehicle from its point of origin to the dealer. It costs approximately the same to get the Toyota FJ Cruiser to the dealership as the Jeep Wrangler.
The Jeep isn't much more expensive than the Toyota FJ Cruiser with respect to MSRP.
Utility
The Jeep Wrangler is likely a better choice than the Toyota with respect to transporting cargo, especially if you frequently need to carry a lot of cargo or sizeable pets.
Neither the Toyota FJ Cruiser nor the Jeep Wrangler has a marked advantage as far as seating capacity.
Towing is significantly more the Toyota FJ Cruiser's forte than it is the Wrangler's.
Comfort
The Wrangler offers more head- and leg-room to your passengers than the Toyota FJ Cruiser does.
Dimensions
The Jeep Wrangler is likely to feel a tad slow because of its high horsepower-to-weight ratio.
Your wallet will hurt more every time you fill up the Jeep Wrangler than the Toyota FJ Cruiser because of its bigger tank.
The Jeep Wrangler and the FJ Cruiser compete for the same parking spaces.
The Toyota FJ Cruiser's shorter wheelbase may produce a less-settled highway ride but a more maneuverable feel in daily traffic than the Jeep Wrangler.
Performance
The Jeep Wrangler is likely to feel somewhat sluggish because of its high horsepower-to-weight ratio.
Handling
The Toyota FJ Cruiser and the Jeep have approximately comparable tires.
Drivetrain
The Jeep and the Toyota have similar-sized engines, with a slight advantage to the Toyota.
Overview
The Wrangler and the Toyota FJ Cruiser have the same basic warranty.