There is a thread running currently..
http://www.gasgasrider.org/forum/showthread.php?t=22742
You need to compare apples to apples. There have been numerous updates to crank volume, port layout, head clearances, etc over the years. There are also a couple different carb models fitted over time as well, and if you go back I'm sure the older engines probably ran different reed valves too. What worked in the early 2000's isn't relevant anymore.
Stock gas gas jetting leaves a lot to be desired. It appears they have an endless supply of N1EF needles and put them into everything. They might work well somewhere, but I haven't found it. Too short on the straight section makes for a hard to set idle. Way too rich on the diameter. Wayyy too rich on the first taper encourages you to lift the needle to clean up off idle. This typically leaves it too lean in the mid range... or you run too rich off idle and it loads up and won't pull clean into the mid top.
Suzuki/Ktm-Yamaha series needles will get you 2 or 3 tapered OEM needles which will allow you to fine tune in half clip positions and any diameter you need, for about $10 a piece.