Stock Rubicons are quite capable. But after one trip to Moab and stacking rocks and heavily using the skid plates to keep up with the other jeeps in the group a bit of an upgrade was needed. There sure are a lot of mall crawling jks with lifts and tires around though. you could do most anything with a 2 inch lift and 33s if you drive correctly (in a 2 door at least, 4 door may need some more for the brakeover angle).
if you started from a stock jeep to sell to get a Rubicon it would be definitely less expensive. As long as you plan to keep with the stock axles. I was about to the point with my yj where I wanted to bump up a tires size flatten the belly pan and get a briefer rear axle when I traded it in on the Rubicon. New jeep fixed all that, the frame and body rust, wore out engine, and the annoying internal clutch slave cylinder issues so all in all a win win.
I don't see why people do muffler relocation its up and out of the way more than the gas tank on a yj or tj. You would rip off the rear bumper before hitting the muffler in my experience. Next I need a front bumper to get a winch and the rear bumper for a tire carrier to support the 35x12.5" spare. Both bumpers have picked fights with rocks and are battle scared anyways.