It's just aged technology.
Just like Dodge. Mopar heads look at the Demon and go "oooohhh, 800 hp" but the reality is, 800 hp from a blown 360 cubic inch motor on RACE FUEL is nothing sexy or special. In fact, it's where the aftermarket/race crowd was 30 years ago. The engine is bloated and inefficient and the car by enlarge is a pig (weighing in a well over 2 tons).
Compare and contrast to the voodoo engine in my Ford that makes 526 hp without a blower or race fuel on a whopping 318 cubic inches.
Newer tech allows engines to do several things.
1) Air/Fuel mapping and spark are CONSTANTLY updated to maximize engine output for the given situation, which takes into account throttle position, intake air temps, rpm, etc to run the spark out to the maximum/optimal advance. It's able to do this by basically bouncing off the knock sensor. It runs the timing advance all the way out until it encounters knock and then pulls the timing back slightly. This optimizes hp/tq and basically makes the engine a constantly updating "tune" like having your own little dyno tuner riding along with you. In fact, my car has to "learn" the tune after being driven for some time after the parameters are tweaked.
The 4Runner's engine does this, within reasonable limits for reliability.
2) Modern internals and component parts help engines rev higher. More RPM's (when combined with proper intake) means more power. The intakes now are crafty and able to adjust runner length again, optimizing based upon the driving conditions.
Higher revs are not needed, nor wanted in the 4Runner to make more power. Varible length intake manifolds have been used in production cars since the '90s
3) Variable cam timing allows the engine to adjust cam parameters based again, upon other inputs. So down low, where classic "lopey cams" would create a rough idle, the engine can adjust the cam overlap and duration to make for a smooth engine run. Then, as rpms increase it can increase the overlap and duration to behave like a high performance cam. This is essentially the best of both worlds as you get the high hp of a race type cam, but the engine idling of a stock/oem type cam. Guys even run a "cam tune" that simulates the lopey idle of an old school race came (which artificially turns off the feature at idle, ironically making the engine less optimal, but it sounds cool).
We've already got dual VVT-I
Newer developments are even coming about with variable stroke length. This will allow the engine to have a long stroke (for torque) or a very short stroke (for high revving and hp).
This is fairly new from the Infiniti VC-Turbo engine, although I understand its a really old concept that just couldn't be implement very well prior. Time will tell on durability though, and Toyota is also implementing Atkinson cycle.
All this stuff is great, but it's disrupted technology. In 20 years, combustion engines are probably going to be the minority as electric engines solve the issues of range and recharge time (and lower costs due to improved manufacturing, batteries,) and weight.
This might be the case.
Bottom line is that Toyota is living off some obsolete tech and they can do this because as I've posted before, fuel has remained relatively cheap and will continue to do so for a long time. Toyota doesn't care as much about power output numbers because their vehicles aren't competing in those segments. "just enough" is the mantra for Toyota and power. And as far as economy goes, again, they were once class leading, but are now just competitive and don't have to invest in new tech as long as fuel stays cheap.
Toyota 4Runner tech is far from obsolete, although they do tend to err on the side of caution for the sake of reliability. You can't really have both bleeding edge tech and proven bulletproof reliability. The engine performance/efficiency could definitely benefit from Turbo-DI but, again, at the price of reliability.
Like I said in earlier posts, I think Toyota will field a new trans before they adopt a whole new engine platform. And if they're SMART, they're probably working on electric and hybrid tech and not dumping money into a dying internal combustion powertrain.
Until I see BSFC maps comparing all these engines, I won't jump to the conclusion that the 1GR-FE is incredibly inefficient. I think it has more to do with lack of gearing in the transmission, weight, and aerodynamics.