This is my third 4runner and I've also owned about 20 other cars and I'm only 33 years old, (I'm a car nut), many of them purchased new. (until I got married wife put an end to that). You are absolutely right with all of your observations. Couple things tho.
1. Stock tires are so bad, you almost have to replace them with something better. Significant difference with handling and marshmellowness. Wheels need 1-2" more offset also.
2. Stock springs are so soft, too soft for any tongue weight at all really. My 1200 pound Yamaha Rhino and single axle trailer (2000lbs) squat the rear 1.5". You have to do a lift with heavier duty springs and prob shocks too if you're going off road or towing. I'm currently researching combos trying to decide.
3. Interior lights are weird, no way around that one.
4. Look at the Yen vs. the US Dollar. $33,000 in 2011 is around $23,000 in 2004 in yen vs. dollar purchasing power. To keep the price point about the same and still be built in Japan at one of the best factories on the planet, Toyota had to strip some things from the platform and cut some corners. It's just economics. Adjust the current price and it's a bargain compared to years past. If the base 4th gen in 2004 was $29k it would be about $38k in today's dollars with the exchange rate the way it is.
5. Reliability and resale. Awesome. You will be stoked some day when you sell your 4R how much value it retained and how reliable it has been, I promise. Especially if you've ever bought a new American car...!
6. Engine responsiveness gets better with age. I swear when mine was new (under 1k miles) it felt like I had to floor it all the time too. It "loosens up" with time and gets more responsive, I don't know the tech behind it, but it does, have patience.
7. Upgrade the front dash speakers to the 3.5 Infinity speakers all the guys on here are doing. They are like $60 shipped on amazon and sound great, easy to install. Then always use party mode. It sounds dang nice.
8. Front wheel caster angle is not set right from the factory. 5th gen's are hard to keep in the lane and drive twitchy on the freeway. Tires helped. KDSS or XREAS helps but I don't have it on my SR5. I'm hoping stiffer springs and better shocks help too, we'll see. After the lift I'm going to take it to an alignment place where they know what they're doing and have them set max positive caster, I think it's 4 degrees or something. That's another reason I want to lift the front 2.5" max, so there's enough adjustment left to set the max caster without having to buy aftermarket upper control arms. I'm trying to get springs to lift 2.5/1.5". Thinking OME 889 with SAW rear coils. Or maybe OW 2.0 coil-overs and rear SAW springs...?
I'll admit Toyota screwed up on a few things with the 5th gen. And it sucks you have to go out and spend money to make it right - how it shouldv'e come from the factory. I'm a little pissed to be honest still. But I studied this forum and knew what I was getting into before hand. A few mods and you'll have a 250K mile vehicle that will retain tons of value and is super safe and reliable and will become like an old friend.
My 2 cents.