I have owned many Jeeps over the years (7), I was a die hard Jeep fan boy. All but two have had major issues, one of which was bought back under Lemon Law in under 9 months from new. Jeeps are out of the box ready and they are like Lego's for adults, so many options and possibilities to modify it however you see fit. I love the solid axles, the lockers, low range, they are modern billy goats. Reliability is certainly a topic for debate as far I am concerned and they don't have the same build quality as a Japanese built Toyota like the 4Runner and Lexus GX.
The 4Runner has bad front-end brake dive (fixed with suspension upgrade), the 5-speed never seems to be in the right gear (could use the 6-speed from the GX) and the 4.0L V6 while reliable is kinda gutless when paired with it's 5-speed. It will get worse fuel economy than the JKU/JLU and the seats aren't the best IMHO. Change the oil, rotate the tires, and hit your major services and it'll run 300K miles without much fuss. Aftermarket isn't as good as it is for the Jeep but it's not far behind when it comes to the 5th Gen. It will be more livable and comfortable on the highway than the Jeep but not by leaps and bounds.
Now you can't swing a dead cat around here without hitting a handful of either of these vehicles. Here in Texas both the Jeep Wrangler and Toyota 4Runner are at nearly every intersection, their popularity is a little hard to stomach at times and it sort of waters down their appeal. We had three 5th Gen 4Runners before we picked up our GX460. We liked the size and capability of the 4Runner but we wanted a better drivetrain and more comfort and the GX is exactly that. With that said, there are a metric $hit ton of GX's here in Texas as well but you rarely come across one modified (that's changing slowly with their recent surge in popularity with this crowd).
With both being so similar in size and price it boils down to your on-road needs IMHO and your perceived value and importance in regards to reliability and the peace of mind that comes with that. I recommend a TRD Off-Road (the TRD Pro has gotten far too expensive for such little difference) so that you get the rear locker and crawl control systems. You've had the Jeep, maybe try the other flavor and pick up a 4Runner. The good thing is should y'all not really gel with it then you'll likely be able to get a large majority of your money back rather easily since they hold their value extremely well. Sell it and get back into a Jeep and move along. Seems like a win-win scenario if you ask me.