I think the best thing for 3.9 is fully working TCP/IP stack. With 3.5 you only got time limited demo version. There are some discussions about legality of the 3.9's stack, but that doesn't change the fact that you got it and it's the best stack for most
Oh and other stuff which you should have paid getting separately like CacheCDFS, Amplifier, XAD etc. Those things made it worth for me at the time, not particularly the OS itself (I was/am Magellan2 user anyway).
