Just upgraded to 3.9. I've observed the same issue with data connection first posted by Daekin: after a sleep, WIFI connection seems to be OK, but no data is transferred. In some cases, I've been able to recover data connection by switching off-on WIFI, but in others, the only solution has been a complete reboot.
As announced, I've tested native WIFI tethering in this version: no success and causes spontaneous phone reboot.
Tests with third party tools (will update):
Barnacle: -without "skip wpa_suplicant": no success and phone reboot
-with "skip wpa_supplicant": wifi tethering active and AD-HOC network visible in the PC, but connection attempt last forever.
UPDATE: Good News! Barnacle with "skip wpa_supplicant" running OK. The problem in my first test was that I made it after trying native WIFI Thetering: from this point on, "Router WIFI" option in "Networks and Connections" showed "Error" instead of "Active" or "Inactive", even after rebooting the phone. I have to restart Router WIFI option, enable it and quickly disable it (before the phone reboot by itself) so the the option shows "Inactive" again. After that, Barnacle works fine. The only issue is that wifi must be reenabled manually after using it, but this is a minor issue.
So the message is: Don't try to activate native Router WIFI in this rom; you'll get stucked in problems!