"Not really wtf factoryX,I have an 02,which is basically the same as your bike,and it's a lot different from the new one.It's sounds good to say I have the same as a new bike,but there are many changes throughout year to year that have improved it to where it is now.The many differences between '13 and mine are obvious when you have actually seen one in person."
03 had a frame geometry change, 04 48mm KYB open chamber vs the 46mm on the 03, 05 Aluminum frame same geometry as the 03 but two lbs lighter, SST forks, 06 everything the same except the SSS forks/shock, 07-10 same bike no changes except maybe front fork axle, 11-12 detuned motor, yzf front axle. The rest is minor and will bolt up no problem. No really, same exact bike. The pipe will interchange 02-2013, some even say that the earlier 99 pipes swap as well. You could build an low 02-03-04 yz250 using new parts, and still be under the actual cost of a new bike that you'll have to fix due to yamaha plugging it up.
KTM 250sx with SSS forks would blow it out of the water.