Comparing a 3-Series to a Lexus IS is like comparing a Mustang to an Altima coupe. Yes, they both have two doors but that doesn't mean they are competition. BMW first of all doesn't even consider themselves a luxury automaker and prides themselves on driving performance. Lexus on the other hand makes cars that focus on luxury, comfort, and reliability. That's not to say that Lexus cars are not agile or fast because they are but they offer a level of quality, reliability, and comfort that the other luxury marques can't match. Lastly, on your points about Japanese Supercars, the GT-R smacks down everything you just said do your research on it.
You don't know what you're talking about. Let's just say, when you were playing them on Playstation 2, I was driving them in real life. I have an SCCA license, raced half the road courses in the N.E. and Mid-Atlantic, and been through more heat cycled tires than you have condoms. Trust.
First, BMW considers themselves a premium brand. Lexus considers themselves a luxury alternative brand, so right there you have a difference in philosophy.
To your point, do you research - Lexus realized the best selling entry level luxury car in the world is the BMW 3-Series and Lexus who goal was to benchmark IS300 against it. It's whole reason for being in exsistence was to steal sales from BMW and create a new entry level luxury sport sedan for Lex. Thus the reason they went for to an inline six engine and rear wheel drive. Until then, no Toyota luxury sedan product used an inline six and RWD - they just duplicated BMW's formula.
As to the GT-R, it's a great car. I was the first to post what kind of beast it was going to be 2 years ago when the specs were released, but bear in mind - it's not the END ALL BE ALL. Again, the GT-R was benchmarked against the 911 Turbo and designed to beat that car first and foremost. They wanted to take a bite out of Porsche sales which has always been considered the "every exotic" sports car.
Now for what it has in techno wizardry, slick tranny, and grip and holding it trades off for being a HEAVY CAR first, and second being a little too computer controlled. Top drivers are saying it's so "smart" it makes you feel like you don't need to be there - like the car would rather not have you drive it since you're just messing up the computers guidance.
Again, like Lexus, and Honda, it's the tragic Achilles heel in Japanese cars - they engineer out the excitement and tactile feedback. It's the difference between a fast car and a fast "driver's car."
That's why I respect the NSX so much. It was a very capable and involving car. And that was because as opposed to letting engineers drive the development, Honda had Aryton Senna intimately involved with design and feedback and driving dynamic.