I've owned several of each. A CJ7, 2 door JK and a few JKUs. All I can do is share my opinion/perspective. I love the look of a 2 door on 35s, and the capabilities. In the end, I'll always own a JKU. The wheelbase has more advantages than disadvantages as far as ride quality, comfort, room for gear, etc. I daily drive my Jeeps and it's nice having room for family, friends, colleagues, gear, and generally just shit life brings up. Getting the kids into the back seat of my 2 doors was a pain in the ass, and I ended up just not running one. It was basically a 1 seater. Ultimately, it was the significant difference of ride quality on the road, where I drive it every day, that made the decision easy.
Off road, an unlimited will have a break over disadvantage to a 2 door, but as I'm sure you've seen here, there are ways to work with that to do as much hardcore wheeling as you want. An unlimited will have advantages of stability at speed, climbs, descents, and seem to fare better on big ledges as well.
If it were me, I'd figure out first if I need or want the room, and what type of wheeling I'd be doing. Obviously, I chose to stick with 4 doors for my personal situation. Good lick and let us know what you decide!
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