To each his own but I've had both and if I had to do it again I'd buy another Rubicon. And I just ordered Dynatrac axles and have coil overs etc so I have gotten rid of a bunch of stuff. Don't discount the value of resale Rubicon parts. Just some comments on a few things.
1) Transfer case - going rate seems to be about $500 + your stock Sport tcase
2) Axles - I sold my stock Rubicon axles as a set with only c gussets on the front and EVO rockstars on the back for $3k. Good luck even selling your Sport D30.
3) Sway bar disconnect - this thing is more useful then many people make out. Seen them sell from as low as $500 to as high as $1000.
4) wheels, tires, suspension - I got a pretty decent price for selling someone who just wanted the Rubicon look the whole package.
5) features - one of the best things about the JK is the ability to use it as a daily driver even when heavily modified. Mine is on Beadlocks and 37s and it is my only vehicle. That said the Rubicon has many features standard that you cannot even get on a Sport. Many others you have to get a Sahara or Rubicon to get them. Nav, remote start, body color flares, and many more. If you are looking at new ones the Sport doesn't have the fancy EVIC that shows you speed digitally, individual tire pressures, trans temp, oil pressure, etc.
Each person has their own views but getting the Rubicon up front you can space out your mods over a greater timeframe and you can sell the parts you remove if you eventually do very easily. That and you'd be amazed what a stock Rubicon will do. He'll what a stock JK period will do. I ran a stock 4 door sport without lockers in Moab last year and you definitely notice the lack of ground clearance but I had no problem having a great time wheeling it.
Just my 2c, take it or leave it.