First of all, disable VAD is always good thing to do.
According my experience, I did not notice any voice quality compare G711 and G729 under a health network and proper installation.
If you have limited bandwidth through WAN, I suggest use G729 with compression, if you have a lot of bandwidth, it really doesnt matter what codec you use.
Remember, follow the SRDN for QoS and Callmanager design base on the situation you have for different customer...
Just my 5 cents. Good luck :)
Ken