I have used both OS3.9 on my 060 seems a little faster. It is far more stable with less problems. Some great added features some not so great but this based on my personal demands and the things I do not like are gone.
Internet stuff is great both have AWeb (no GPL and program can DL'd and installed with no limit. comes with mail but in fact most would use Yam or Simple Mail.. As far as the stack goes Yes 3.9 has Genises but with high speed in North America it is usless as all High Speed ISP's here seem to use DHCP which is not supported by Denises and has never been addressed by H&P in upgrades. Miami and Miami DX do have support for DHCP. But I am assuming if you all ready go on line with your Amiga you already have a full stack so stay with that.