[T-Mobile Samsung Galaxy S II SGH-T989] monkeybuttons:
I have noticed a few people complaining of call echo with AOSP ROMs (even with "noise suppression" checked), as well as some stock based ROMs. I was having the same problems. Stock based ROMs were better, but echo was still there. I tried several radios without avail.

What finally worked for me was going back to stock through Kies (keep in mind this will wipe your internal sd as well, so move your backups off your phone). I have since been able to flash PACman ROM without call echo. I have not tried any others but I assume the result would be the same. If someone is willing to test other ROMs/radios and report back that would be great. I just don't have the time.

Also, I did not flash a different radio after going back to stock. I assume it would be okay to do so, but I am not a dev so that is only a guess. What I think going back to stock fixes is some missing/corrupted libraries that are somehow surviving ROM flashes (like in a protected storage or something like that).

Anyway, I hope this helps someone else.

EDIT: This doesn't work all the time, and has only really worked for me once. I have done it twice and it worked great the first time, and not really the second. It's worth a shot, but just keep this in mind.

:::Specifics:::

Essentially all I did was go to the latest stock rom image from T-Mobile. Kies upgraded my phone to UVLI1, which is T-Mobile's latest 4.0.4 stock rom. Kies essentially wiped everything from my phone (except external storage) and imaged it with the latest factory image which includes the latest radio. I have since been able to root, install TWRP and flash an AOSP based rom without degradation in call quality. I did not flash over the radio that was installed by Kies, and I did not wipe android secure in TWRP (don't know if that made a difference).

What you should try if you are having call quality issues:

1. Go back to stock unrooted (use your method of choice, I used Kies but that doesn't work for everyone so try Odin or Heimdall)

2. If you didn't go to the latest stock unrooted image from T-Mobile and Samsung, do that through Kies which should now work for almost everyone (as of Jan. 1, 2013, the latest stock image is UVLI1/TMBLI1)

3. You should now be able to root and flash any rom you like without call quality degradation (if this is not true for you please let me know --- see above for what I did at this point)

I'd be interested in getting some feedback from this. Keep in mind that I am not always available and may only be able to reply once a day or less. Again, this is just what worked for me, it may not work for you. Please give yourself plenty of time when going through this process as Kies is not very fast (at least in my opinion).

UPDATE:

Here is how I got Kies to update my phone while still rooted and even running an AOSP rom. As always, do this at your own risk. I accept no responsibility for broken devices or lost data/pictures/music/etc. However, I have done this twice now, so just read and understand what you're doing and you should be fine.

Keep in mind that this WILL WIPE YOUR INTERNAL STORAGE! You have been warned.

1. Disconnect your phone from your computer

2. Launch Kies and click on Tools>Firmware Upgrade and Installation

3. Input model number (it's case sensitive !?) and hit OK

4. Input serial number (found under battery) and hit OK

5. Hit okay on windows until it starts downloading the latest firmware for your phone

6. After it's finished downloading it will tell you to put your phone in download mode and connect it to your computer. Do it, check "I understand..." and hit OK (I also opted out of the sending of information to Samsung)

7. Wait until it's finished. It will likely launch a window saying it's downloading a file for emergency recovery of your device.

8. When it's (finally) done it will tell you it was successful (hopefully). Your phone will automatically reboot and all will be well with the world and your phone.

Hope this helps.