I don't really want to debate the whole IFS vs live axle thing again, but I was present and spotting when the first 100 series (and an IFS 4Runner who has since swapped in a SFA!) went through the Rubicon along with a bunch of 80 series. Your friendly moderator was there too. All the rigs were close to equivalent--locked on both ends, 35 inch tires, 3+ inches of lift. The SFA trucks were MUCH easier to get through. The reason is that when a tire goes up on a rock, it takes the entire axle, differential, and truck body up with it, which in turn magnifies your ground clearence. With IFS, only the tire goes up leaving the rest of the front end closer to what ever it is you are trying to drive over. This is not to mention the weaker components, weaker steering, and vastly increased complexity if a trail repair is needed.
There is no question that IFS is better at high speed, but if you buy an FJC because you think offroading is about high speed, I hope you have a deep wallet and a friendly tow truck driver. While offroading, people pay big money to be able to go slower, not faster! For you FJC owners who are new to this, the 4:1 transfercase of the Jeep is a HUGE advantage. 4Wheel a bit, and then tell me you don't want a deeper low gear. Marlin may be your friend!
There is also no question that the FJC will be a less troublesome vehicle than the Jeep. It's based on the proven and reliable 4Runner, and I would expect no less. It's also likely to be a better street car for trips and the daily commute. Thus, it will make sense over the Jeep for most use. If, however, your goal is 4 and above trails, and you can choose only between the FJC and this proposed Jeep, the Jeep will get the nod.