As others have stated:

1. In-glass antenna (I hate an external antenna)
2. Fuel locking door (I can't believe they removed this!)
3. The V8 option
4. The "self-closing" rear hatch function. (I hate nearly "slamming" my hatch to make sure it closes. Before, it was just get it close and it sucked it shut)
5. The Projector headlights I had in my 4th (and the LED brake lights!)
6. An option to have the CHROME in BLACK.
7. A better rear-window wiper, seriously, can we clean more than 50%??
8. An easy way to remove the rear deck to get space back.
9. The "one turn" key start that the 4th gen has. (I have push button on limited, but my buddy has an SR5. I can't believe Toyota removed that!)
10. Put the automatic climate control back for *ALL* trim levels.

/end rant

This may be a silly thing, but I'd really prefer if the USB-in for the audio system was in the center console. As someone who wants to keep a few flash drives in the car, like you would with CDs, it's kind of obnoxious having to get into the glove to swap them. Imagine having to reach into the glove compartment to switch a CD . . . that would seem insane . . . thus, I find it insane. I appreciate it needs to be in a box somewhere, so you can put your iPod or what have you in there and close it, but the glove box is a little dumb when it could just as easily be the centre console.

You should be able to pull this off using nothing more than a USB extension cable and a little bit of cable fishing.

Yeah, I am probably going to do that. I just don't want to even think of punching holes anywhere yet, hahahaha

For now the extension cable and open glove box might be what I do.

....Everything Kmiller said and

1. Turn dial 4WD activation on the SR5
2. 1 button to roll up/down all windows
3. Run fog lights by themselves

Another one.
- Replace the taillights.

About a 6 speed manual transmission, same as Tacoma

Uhhh... the windows are all one touch.

And another.

Put the Trail headlights on all models.

Buy a USB hard drive, load it up with your music, and leave it in the glove box.

4th gen's 4WD system on all trims.

+1
More useful rear storage
Digital climate control
Down facing Door lights
Better radio interface (I cannot read in direct sun)
Illuminated buttons
Rear wiper upgrade
USB in center console

Everything above + the following:

11. Greater towing capacity (6500lbs at least)
12. Windshield channel to catch windshield washer fluid from running across driver/passenger windows
13. Better aerodynamics on the sunroof to quiet it (too loud inside w/ sunroof open)
14. More sound dampening on the interior (too loud inside)
15. Khaki/Tan carpet......really, you only offer black carpet in all 4Runners?
16. Lower the top of the door panel (I can't rest my elbow on the top part without it being uncomfortable or raising my seat too high)
17. More hidden cargo areas built into the interior
18. Remote start as a pre-installed feature that "doesn't" require you to turn the vehicle off first (WTF)
19. Courtesy Features pre-installed so you don't have to go back to the dealership to get all the extras that should be available the day you drive away
20. Wider stock rims to allow to the option to run wider tires (I like the stock 20's, but can't run the tires I want cause the rims are too narrow)

Have you tried dropping your rear-window an inch or more when your sunroof is open? I do this all the time, and the "rumble" sounds pretty much go away.

1. Automatic Rear Window from my Keyfob (like my Third Gen)
2. Rear Heating Capability (like my third gen)
3. E-Locker in the SR5 (like my third gen)
4. Crotch Vent (like my third gen) or perforated Leather seats w/Air.
5. Lock on fuel door w/internal release (like my third gen)
6. Roof Mounted Rear Cargo Light (like my third gen)
7. Heavier Duty Rear Cargo mat (like my third gen)

Don't get me wrong... I love my 5th Gen... but it seems to be missing many of the nice little "details" from older versions.