FWIW I own a 2 Door '07 JKR 3.8 6 speed with a RIPP, 4.88's on 37's and tons of armor. I also own a bone stock 4 Door '12 JKUR auto 3.6 with 3.73's. The 2 Door (which is much heavier) always pulls away from the 4 Door and though its not dramatic, its noticeable. The 2 Door is especially fun in the sand around Ocotillo and Superstition where the 4 door cant come close to keeping up especially on inclines.
The 2 Door has been on the majority of trails in SoCal as well as the Rubicon and Dusy Ershim. I've had no major issues caused by the RIPP, its biggest downfall is the requirement of 91 fuel and rendering the cruise control useless. The Jeep is a blast to drive on the highway especially up long grades where the power pulls you effortlessly. The RIPP offers little no gain on the rocks, unless your on the throttle in 4Lo; buts its also not designed to increase power in this situation, thats how you break stuff...
I've witnessed many issues with FI systems installed by shops that hadn't had previous experience with these installs. I installed my RIPP which I bought used from a Motech customer getting a LS Swap. I paid $3k shipped for the full RIPP Gen 2 Stage 2 kit, Ripp long tube headers, a running 3.8 and a blown up Level 10 built 42RLE. I sold the motor locally for $1500 and still have the trans sitting around. I installed the RIPP system myself and cleaned up up the top of the 3.8 at the same time changing the intake manifold gasket and ECT. A compression check showed that even at 90k miles my 3.8 cylinders and rings were in good shape.
The biggest difference between the 3.6 and 3.8 is really the transmission not so much the Pentastar. The Mercedes W5A580 is a great transmission and far better than the 42RLE in every way. I was looking for a 6 speed JKU when I bought the '12 but after driving the auto and finding out what vehicles it was used in, I was more than sold.
For $1500 invested, I would say the RIPP is definitely worth it. For anything over $3k, I wouldn't spend the money on it.