I looked into both for a long time, ended up with a JKU Willys package for specific reasons (yes, I know some believe it to be a sticker package). I have to fit my wife, a teenager, a Jack Russell Terrier, and all our camping gear for our trips and it can get challenging fitting it all when I am running my slant back soft top in the summer months. When it comes to space, comfort, and mpg, tow capability...the T4R is the clear winner. I love the new T4R so much that it will probably be my next vehicle once the Jeep is paid off.
So why did I pick the Jeep? It was a better match for my lifestyle and goals for the price. Pure and simple. Many of the pitfalls of the Wrangler are the things I like about it: twitchy steering on the highway feels right to me in a trucklike vehicle and I enjoy the challenge of seeing just how much stuff I can cram into it. We chose the trim level to get the Rubi tires/suspension, a limited slip rear diff, liked the looks (yes, the stickers), and it didn't have anything I didn't want. I overlooked the Dana 30 up front vice the 44 in the Rubi, because I was already planning an axle swap/regear to go with a lift; the lift would cancel out the Elecronic Disco Swaybar, lockers are great, but not $5k-10k great when they leave you with an open diff on an icy/snowy highway unlocked...We added the hardtop (which I recommend to anyone buying a new Jeep, because soft tops are cheaper to buy afterward), slushbox for the wife and an engine block heater...thats it. From the beginning, we wanted something that we could turn into a rig that we could pile our small family into on Friday, go wheeling, get muddy, go camping, fishing, exploring, etc...garden hose it out on Sunday and go to work in it on Monday. Leather, carpet, and drain plugs be damned, lol. But that is us.
The T4R is what I would recommend to most people because it is the perfect vehicle for Monday-Friday with plenty of capacity/capability to play all weekend and you can tow a boat as a bonus. But, IF you end up going with the Jeep, take a look at what your "endgame" is and consider some of the lower trims if you want to save money for mods. Buy what you need so you can build what you want, or spend the extra to buy a finished product and just enjoy it. Let's face it, most Rubi's and TRD's will spend 90% (made up percentage) of their life on the pavement. We ended up at 35 and some change out the door and have 37 total into it now (Rigid/Trucklites headlight upgrade because stock halogen is garbage, CB, Bartact seatcovers for H20 and dog resistance, Rampage frameless softop, overhead storage rack inside, etc). It took us comfortably from Texas to Washington state in the dead of winter during it's first 3-4k miles, and by driving conservative, I wasn't worried when there was noone left but us and the snow plows on the road in Dead Man's Pass through Oregon.
Feel free to hit me up if you have any specific questions and good luck on the purchase, it's always an exciting and exhausting process picking a new toy for your stable.