You're stuck in stone ages, my friend. Sure, direct injection had it's teething issues when it came to the market 15 years ago. Direction injection gives around 10-15% better mpgs and power. The biggest issue with direct injection was carbon buildup on the intake valves which then would require a $500 servicing every 60-100K miles. With the exception of the 4Runner, all Toyota products are direct injection.
As for the 5 speed auto, it is about a archaic as you can get these days. I'm not aware of any new car/truck sold in the last 5 years using a 5 speed auto. Even 6 speeds are considered quite dated. This truck desperately needs more gear ratios to make use of it's powerband which isn't not exactly stellar for a truck, IMO. It's powerband is from 3,500-5,500rpms. The 4Runner would get significantly better mpgs, it would be much quicker from a stop or roll, and would be much better suited to towing with the extra gears and MUCH needed torque multiplication of a 8+ speed auto.
With DI and an 8 speed auto, which Toyota has had available since 2008, and some much needed convenience comforts that have been standard on most every Toyota product in the last 5 to 10 years, and the 5th gen 4Runner would be a class leading body on frame SUV. Toyota is just too damn conservative for their own good. They know how to squeeze blood out of a turnip, that is for sure.