I am not a Wrangler owner yet, but here's what my thought process has been thus far:
Day 1: Man... that new JK is sweet! I gotta get one! Probably should spring for a Rubi.
Month later: Did a ton of research. I went to a local Jeep dealer and got to drive a JK Sport Automatic. Nice Jeep, decent power, feels nimble and fun to drive, turned on a dime. Loved it.
First issue: Fitting a couple of full-sized people in it. It was me (6'1" tall, 280 lbs) and a friend of mine of similar stature, along with the salesman who was not a small man by any means. I felt fine, but my buddy in the back looked a bit cramped.
Second Issue: When I popped the rear glass open, I realized that the JK didn't have a lot of room behind the rear seat. (My C6 Corvette appears to have more available room, to be honest.) I travel quite a bit for my job, so being able to load a couple of suitcases in the back is important... and while I can fold down the rear seat to get the luggage to fit, what happens when I try to load up to go camping? What if I take a couple of friends and all of our gear?
Needless to say, I still like the 2-door JK... it's a great vehicle for sure. But I'm now leaning towards getting a JKU because of the space issue. I'm a single guy with no kids... I can't imagine that you'd be happy with a 2-door with three kids, especially if you ever needed to haul them, their stuff, etc...
As for getting a Rubi or not... you'll get quite a few different opinions about that. Unless you plan on doing some serious wheeling from day one, I don't think you'll be disappointed with a 'regular' JKU.
Good luck with whatever you decide to do.