I think others covered it well. I have a 1999 and 2017, all stock.
The 1999 is more playful, can be slid sideways, 180 turns, nose stabs. I think a lot of this is the steering throw so I should get the 2008+ steering fixed. When trying to turn hard it will either slide and break loose, or the pump comes out of the water and then you lose power and fall over.
The 2008+ handles a LOT better at high speed and when turning. I also notice it cuts small chop well and has zero porpoising. Standing all the way forward on my 1999 doesn't get it to stop porpoising. It carves hard, lean it over and WOT and it just grips. The steering is slower and it is much harder to slide. It is also much easier to ride for new riders, it is very stable. I've taught people that have never been on a ski on these and see the 2008+ is much more forgiving for them. It has a 'chine walk' at low to moderate speed on glass. It has never escalated or thrown me off. Add even the smallest ripple to the water, or just ride aggressive and it's gone. Does not bother me.
I like both skis for different reasons. I probably need to swap the steering cable on my 2017 and I think it would pick up some of the good traits from the 1999 but haven't read a good writeup yet.
I also have a 550sx and 650sx and it's fun that all four skis all handle entirely different. I like both SJ more though, they just feel "dialed" in comparison.