I'll throw in my two cents!
For my budget, what I'd be using it for, and the fact that my wife won't dare but used, I went with a Sport S. The first reason was obviously financial. I couldn't afford to foot the extra money that you have to pay for the Rubicon. I could have bought one used, but after many bad experiences with previously used vehicles, my wife won't have it. Buying a new Rubicon would have made for a higher payment for me which means no room for mods.
My next reason is what I'd be doing with it. Honestly, I had this "dream" whenever I bought my first Jeep back in 2011 that I would actually get out and be a hardcore wheeler. Now, five Jeeps later I realize that is not me and I may wheel 2-3 times a year if I am lucky. So, with my amount of wheeling I knew I couldn't justify the extra prices for the added goodies.
I knew I wasn't going to change out the axles, suspension, transfer case, any of that right away. Even with that though I couldn't justify the price of a new Rubicon. I knew that the biggest size tire I'd run would be a 35" so I knew that I would be "okay" with the D30. Even when I am on the trails, I run the easier lines and play it safe. I know, I am boring. My Jeep is a daily driver first, and champion off road hard core wheeling machine second.
Bottom line is, whenever my sport was stock, I wish I could have had a Rubicon. Now that it's modified how I like it(almost), I wouldn't trade it for anything.