I'll say it again, Lexus is never going to do away with the nav lockout, nor are any of the other companies that have them. You can use the voice commands or install a Prestigious Society upgrade. Those are your only options.
Is the trunk lighting LED on the 460? I don't care for the new LED interior lighting...
Really? The glove box lighting works all the time on my ol' ES.
Lexus vehicles have never had underhood lights...no idea why.
Not a lot of LS460 owners take their own wheels off. I never would.
I don't know why these come and go. The 05=06 ES330 had this also...then the ES350 does not.
No vehicle manufacturer's rearview mirror is linked to the memory system. It would have to be power operated which would make it overly large and heavy to hang on the windshield.
With an adjustable seat and wheel, adjustable pedals are superfluous. The ES300/330 had a power pedal system that was removed when they came out with the ES350 because it has the power tilt/telescoping wheel.
I personally don't want "features" for the sake of having features. I want features that work.
If you want to hold your breath go ahead, I'm not going to.
I think you over-emphasise the number of people that seem to find it an issue like you do.
No car is perfect, and if you expect a car to be perfect and have EVERY feature you possibly could want and still not cost $100,000 you're setting yourself up to be dissapointed. The LS460 is a great car that is extremely well built. If you look past your very minor (and some really silly IMHO like power pedals and a memory rearview mirror) issues your LS460 will be a friend that will actually get better with age unlike most cars.
OR you can pay $25,000 more for an S550 and still not have a lot of the features you mention and have a car that is going to need a lot more maintenance and repair throughout its life. I'd rather buy an LS460 and another little car to zip around in for fun than buy one S550.