I am a Nikon user as well, but I know that the built in Canon system does rely on line-of-sight, the same as the Nikon system. I have used the Nikon system a bit and it definitely has its limitations. It will not work reliably with the slave flash anywhere that would not be illuminated by the built in flash. Range is limited by this as well and even more so in bright sunlight. The nice thing about the system is that it does support TTL flash metering.
Dennis mentioned the newer PWs that support TTL (MiniTT1 and FlexTT5). If you have the PlusII or MultiMax realize that you must use manual flash settings.
I have not gone the way of the PW because I want to experiment with the built in system and learn more about off camera flash techniques before spending the money on the PWs. In your case it looks like you are a portrait photographer and I don't think you would want to deal with the lack of reliability of the line of sight system.
So, long story short, in my opinion, keep the Pocket Wizards, or if you want the TTL and didnt get the Flex and Mini, exchange them.