Apple licenses the traffic data from Waze so (in theory) the results should be the same but, considering the differences in POI between Apple Maps and Yelp or Tom Tom, I doubt that's the case.
... and that's ignoring Waze's ability to alert you of traffic, various hazards and incidents up ahead whereas Apple's doesn't even let you see traffic from the Navigation screen.
I used Waze a lot before iOS 6, and contributed to its maps quite a bit (their maps are terrible). The biggest problem I had with Waze was the number of false positives on police, traffic, accidents, etc. It is nice to get warning from drivers up ahead, but in my experience, 80% of the time the problem was no longer there. This was especially true of police. I guess people were reporting police driving on roads, instead of speed traps, etc. Great idea, but I started to not believe it after a while.
Actually, an even bigger problem was safety. I found myself trying to report things as I was driving. It's as dangerous as texting. I had to give it up because of that. It actually sold me on Apple's apparent decision to make its maps a "headless" system (as opposed to a more HUD type system that all other vendors have).
I now keep my eyes on the road, not on my phone (unless I want a quick glance at the turn or the distance). I'm not looking at the screen to decipher traffic colors on a route, my current speed, or POIs, etc.
I can't overstate how nice it is. If my kids were old enough to drive, I would not give them anything other than an iPhone (if anything at all). I would probably get a car with the upcoming eyes-free system.