First, let me start by saying no one will be able to give you a proper answer short of an R&D engineer or project manager at Toyota Corporate (in Japan). Good luck getting a hold of one, attempting to communicate and getting a straight answer. In the meantime, all we can offer are possible explanations of why; basically, conjecture. I’m going to limit my discussion here to the 4th and 5th gen because they’re really the only ones relevant to your post since they’re the most recent.
In your thread in the 5th gen section (
http://www.toyota-4runner.org/5th-gen-t4rs/185161-must-decide-toyota-4runner-vs-highlander.html), KidV gave a good explanation as to why you shouldn’t classify the 4Runner – especially 4th and 5th gens as made for “off-road.” They were designed for the masses (family haulers, mild towing, mall crawlers, etc.) with nods to its off-road heritage. For high volume manufacturers, vehicle development and design pretty much comes down to two things: meeting regulations and making money. In 2014, only 3.7% of all new vehicles sold in the U.S. were manuals and only 1.1% of all “trucks” were manuals (
source; table 5.3.1, pg. 80 and table 5.3.3. pg. 82). Here’s an interesting article, written by someone with real life automotive manufacturing experience:
Why Manual Transmissions...Are a Challenge. The tl;dr version is this – with today’s regulations and requirements, it’s cheaper and less risky to make a more complex automatic than it is to make a manual for the same vehicle. Knowing the above, would it make sense to spend time and money to make one fit and available in America?
The market here doesn’t stand for manuals the same way it used to. Unless Toyota owns 100% of the BOF, off-road SUV market, it would not make sense to cater to the small crowd who would want a manual $35k to $45k SUV, and the even smaller crowd that would buy a manual $35k to $45k SUV, modify it, and beat it up off road.
Are the 4th and 5th gens capable off road? There are a ton of build threads on this forum that prove just that. Do you absolutely need a manual to control torque to the wheels? No, but even if you did, Toyota wouldn’t make money. You'll find a new manual SUV with Toyota in the FJ (discontinued after 2014 model year). Otherwise you've got a small handful of makes and models to choose from (including the Jeeps, which come with another host of issues).
OA