V8 option, first and foremost. V6 is great, but some of us want more, especially for towing boats and trailers. Locking diffs, front and rear! Higher stock suspension that allows larger tires out of the gate, or an electronic adjustable suspension like the Lexus GX470. More protection in the form of skid plates and solid bumpers. A nice STURDY stock roof rack that isn't curved and will hold a roof top tent or retractable awning without a fuss. The FJ cruiser and Nissan Xterra came with nice stock roof racks, why cant we get something like that on a 4Runner, even if it's just an option.
If people want a luxury SUV meant for strictly highway driving and commuting, there are options out there, and a Limited 4runner can provide that. But most of us buy 4runners because we want a SOLID, and dependable 4WD body on frame vehicle that will take us anywhere with the upmost confidence and leave a grin on our face. I know Toyota can provide that if they really wanna get serious.
That being said, having all of these options out the gate would be great, but the aftermarket will continue to thrive on Toyota's "shortcomings", and many of us take pride and enjoy building up our trucks and making them unique. So either way, I'll be happy. Some more offroad oriented options would be nice, but at the end of the day I'm going to mod it out anyway and make the vehicle as off-road worth as my budget will allow