I like the LED taillights better on the '06+ 4Runners (which is why I got myself a pair) and the projector headlights are nice, but why did Toyota have to get rid of the projector foglights? Those I like much better on the '03-'05 models.
I also prefer the '03-'05 grille and front bumper over the '06+ models, however, I've never been a fan of the rear bumper lenses, so the '06+ rear bumper looks better to me.
The one thing I absolutely hate about the '06+ models is the way the tires sit so far inside the fender flares as compared to the '03-'05 models. The tires look like they should be moved out about two inches to make them more flush with the side of the body! What was Toyota thinking when they did that???