I hear what you're saying, but the point is that it's not a 'manual' mode on the Lexus 250, it's a 'sports' mode.
I understand that it might have some use to assist with braking, but is that really necessary? Personally, I'd rather let the brake pads take the strain than the gearbox. However, I know people who'd disagree with me.
I use it to assist with downhill braking, e.g. in a 40 mph zone if you start going downhill the car will speed up and unless you brake, will exceed the limit (watch out for those speed cameras!). So i'll often switch into S and immediately downshift into 3rd. I don't like braking all the way down a gentle hill, it wears out the brake pads, gets load of brake dust on your alloys, and annoys people behind who are in the 'correct' gear. It won't wear out the gearbox doing this, the braking effect comes from the engine.
What i would really like would be the ability to down/up shift manually without having to move the lever into S - i believe you can do this in some BMWs. The gearbox would have to be pretty smart though, otherwise it'll just shift back up or down again immediately!
Oh, and for extra sports 'shove, i switch the sports mode button on - you know the one that's completely hidden by the steering wheel and which you have to feel for...... :duh: