I've had my 1999 IS 200 SE for about 3 weeks.
1. Auto lock: not sure everyone wants it. What actual advantage does it serve? If you scared of car hijacking or a robbery then maybe. Otherwise I can only see issues like the doors being locked if you're in an accident. I know lots of cars have this feature, it's not one that I think has a use. Like you said for the mirrors, you can press the button if you want anyway.
2. Coin box: There are plenty of places you can put a few coins, they just don't say 'COINS' on them. Mine are in the front ash tray.
3. Auto-folding Mirrors: Yeah, would be useful, but fold in when you press lock on the fob not on engine off. It's also not as simple as an extra line of code. Sure, software wise, it is simple. But there will need to be an extra control line/relay etc, so a bit of hardware required.
4. Handbrake: I thought the handbrake position looked a bit weird, but using it has been fine. It's over to the left so it's not in the way of your arm for changing gear. Most cars have it further back, or my last one did.
5. Mudflaps: come on, no mudflaps, is this a design error? Or did you forget to get the option.
6. Headlight alarm: Mine has an alarm.
I'm sure they did think about all these things. And personally, I think they chose correct on most of them. I find the auto lights don't come on soon enough for me either, and so far that's the only niggle I've got. (Other than niggles with the car not being new, of which there are plenty!)
Rich.