I beg to differ. Stock for stock, the 4 door is a hopeless turd compared to a 2 door. The 4 door is constantly dragging its belly and is much more difficult to maneuver, not to mention the weight penalty. I rented a 4 door JK once in Moab with a 2" spacer lift and 33" tires, and it shocked me how many things it would scrape and drag over that I would never give a second thought going over in a similarly modified TJ.
Modified on 35-37" tires (assuming you are locked into keeping the stock wheelbase) it is a bit of a 6 in one, half dozen in the other scenario. The 2 door will eat the 4 door's lunch on tight, technical, boulder-strewn trails like I typically run, but the 4 door will have an advantage on really steep climbs in open areas with gentle break overs (Moab).
This. In my opinion 100-110" is the sweet spot (105"-110" if your focus is more on steep climbs and water falls than technical boulders). Obviously little to no front or rear over hang is ideal, which you won't get with a reasonable wheelbase in a 4 door. 118" (JL Unlimited) is just too long. Sure, there are plenty of very capable JL Unlimiteds out there, but their length is a hinderance.
I'd personally I'd still take the 2 door in that scenario. The 4 door doesn't really start to run away from a stock wheel base 2 door until you get into the 37"+ tire level.