Not really. You could put the plastic on the front like some do. You could put a bug shield on it to protect the leading edge of the hood. Nothing you do though is going to stop that small stone kicked up by the truck in front of you from scratching or denting the paint. Door dings and chips happen even to the best paint jobs on the planet. If you don't want anything to happen then the best thing to do is garage it and never drive it.
As far as this being a collector's item? I have read this statement and sure, maybe it will be but not for 40-50 years. A Datsun 240Z from the early 70's (even the rare models in mint condition) can be picked up for around 30K. That's 45 years old! The Lamborghini LM002 SUV is rare. There were 321 sold in the US. It cost $120K new. A perfect 1982 example with only 5K miles sold for $170K. The vehicle is 33 years old!
Yes, it's badass looking now. There will soon be "the next big thing" though that will make our 4Runners look old and dated. Every now and then a vehicle is produced that will transcend time and still be beautiful 50 years from now. A Thunderbird, a Corvette Stingray or a Ferrari 250. Is the 4Runner TRD Pro one? I doubt it but we'll see.
I know there will be a 2016 TRD Pro. There will be two new colors and the Inferno will be temporarily retired. FJ Cruisers did the same with the Trail Teams versions.
Personally I just drive mine knowing it is going to get scratched, dinged and dirty. To me it adds character, sort of like a scar but I have had many new vehicles. I understand your frustration but a vehicle is not made to look perfect for a long time. Any vehicle. Could they give it a coating that wouldn't scratch or chip? Sure they could but do you want to pay $50K for that coating? Nobody else does either.