The main advantages of OS3.5/3.9 are the TCP/IP stack, large HD support, CDFS, and other support software. If none of this interests you, then stick to OS3.0/3.1.
Plus things as integrated deficons, newicons, integrated search function, async wb, improved datatypes that make it much more useful than 3.0/3.1.. everyone with 3.1 roms really should get OS3.9, its well worth its money..