I had the iOS 6 GM before it went public and had recently started a new job and now need navigation on a daily basis, so I put Waze and Apple Maps to the test and here's my advice:
Go with Waze for now. Apple Maps has a lot of potential, it's got great interface and design, BUT... the issues that I had with it is the lack of navigation optimization (you can't choose to avoid tolls or minimize turns or avoid highways, etc) while Waze does have those features. Also, the way Waze displays upcoming turns, directions, ETA, distance left, etc. is more well-placed on the screen than Apple Maps. I had trouble reading some of the finer text on Apple Maps while it was in my car mount, while Waze is no problem from any distance. As far as voice navigation, Apple Maps tended to be usually more specific (it guided me within a smaller set of roads within a large parking lot, as opposed to Waze which said "you've arrived" when I didn't even pull in to the parking lot yet). I personally avoid tolls so Waze is the right one for me. But Apple Maps is very well designed and has a great interface.