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I assume your '06 has the 18" wheels? Thats really the difference. My Dad had a 98 and an 04, the 04 was a UL with 17s and the rides were very similar. I drove a ton of LS430s when I was looking at a CPO one some years back and the 18s have a big impact on the ride.
Actually we're talking same wheels, same tires... (see pic above).
Years ago when my LS400 was all stock, the ride was great on my 16' Primacy mxv4. When I went to 18s with Bstone Serenity+ tires, the ride was even better (I guess the new tires offset the harshness of a larger wheel)
When I got my LS430, I drove 1000 miles with the orig 18" wheels and Goodyear Eagle RSa.. ride was ok. Switched my Serenitys on (10k wear) and it does not feel as smooth as when they were on the LS400.
Issue seems to be suspension as opposed to rim size, tire wear, brand, etc.
They both have beautiful styles. I still see some LS 400 vehicles around and virtually all look fantastic. I have the o2LS430 and believe it has a timeless design. You cant go wrong with either one. BTW I also have an 08 LS460 and also love that design.
I first fell in love with the 98-00 body and wanted one for the longest time but the 04-06 body style kept drawing me in and now is my favorite, hence I own one now! I still love the front end of the 98-00.
I drove a blk/blk w/ chromes 96 LS for 7 years and loved it. I just bought a blk/blk w/ chromes 06 LS. The 06 looks and drives much bigger and now looks much more current than the 96 or even the 2000 body style.
They are both wonderful cars.