The first and second gears are for braking not doing 0-60 times. When you are in D drive and doing about 70 and flick the gear stick to 2 postition you get engine breaking to help slow this big car and if thats not enough to stop you then flick it to 1st postion for even more engine breaking at around 30mph or less.
To pull away quick just select the power button and shove the pedal to the floor with a double motion, This will then give you good accelaration. Some good tyres will ahel along with strut braces for faster corning. Wider alloys with more rubber helps, But at the end of the day it's a luxury car not a sports car.
You can get some air intakes and supercharger kit for 400 horsepower, It's about £3500 UK pounds for the kit.
Maybe I misunderstand but.... In D it will still use first gear first, followed by second etc and the original poster is referring to slow pickup in first gear and getting better power once it changes to second?? So he is wondering if he has a problem with first gear??
I though the 0-100km/h for the LS400 was quicker than the GS300 so I would say 9 seconds seems a bit slow. However, no idea what the problem might be other than maybe a fluid change is in order for the gearbox.