Great thread! Am in the same quandry. Currently own a TJ and looking to get a new JKU only because of the pentastar - else i would have preferred a nicer '08 onwards.
Anyway, my mission is simply scenic overlanding with the wife, no rockcrawling (not until i get my money's worth from the overlanding). Wife and i love the Rubi in the khaki color but am finding the $40k price a bit hard to swallow. Likely will go with the base Sport and use the $7k savings for minor armor and camping luxuries. As i learn more about overlanding, am sure i can justify and future mods i need to make for particular trips.
The khaki color (Sahara Tan) is no longer in production so if that is a color you want you will have a hunt on your hands.
This topic seems to be mainly about choosing 2 brand new vehicles, but if cost savings is why the OP is considering a modified sport over a Rubicon then of course the obvious answer is to buy a used Jeep. They do hold their resale value extremely well so you might get sticker shock when pricing used Jeeps but if you search long enough you will find a good deal. Like I mentioned earlier in another post used Rubicons are even cheaper than used Sports relative to new MSRP.
A lot of Jeeps are second vehicles or pleasure vehicles and you can find many with really low miles that have been well maintained. My 07 only had 32k on it when I bought it a few months ago. I was able to get a really good deal on mine because the soft top was not in the greatest shape and it was obviously taken to the beach fairly often. I'm still getting all the beach sand out of it! I paid 16k for it and bought a used soft top in like new condition for $200 on craigslist. Keep looking and you can find a great deal.