There've been a lot of post with people saying that the two programs have been the same app, however, the two are very different in the way they function. Navigation had a large, clear orthographic view, street names were easily readable, traffic indications were bold and distinct, two touches could reroute, three could turn off highways or toll ways. Also, in my case, I often did not use Navigation for point to point routing, usually when I got into the car or on the bike, I'd simply turn it on and run it in map mode. This let me easily see street names and intersections without having to put in a destination, again, in an easily readable orthographic display that scaled based on speed.
People also have said that everything in Navigation is still there in Maps..it isn't. Maps can do an orthographic mode, but the street names are tiny and can't be easily read with a glance, if you want to pull over every time you want to see what a side street is that doesn't have a sign, more power to you. Also, it's following when I experimented with it was very choppy, and always slanted at about a 45 degree angle to direction of travel. As mentioned before, traffic indication is now tiny and subtle, if you're mostly color blind like I am, it's another thing that's useless when driving.
I liked the navigation application, it was smooth, reliable, cached route data for a trip so that it would run without network if you already had a route planned, and it was free. I also figured that if data was being pulled directly from the network, you'd always have the most up to date information available (though, honestly, I have no idea how often they update on the server side). It was an application that I literally used every day, when I got into the car or on the bike, I'd pop the phone into the cradle, start up music, and start up Navigation. I'm annoyed that an application that I relied upon was pulled out of the blue. True, I wasn't paying for it, but I relied on it. Now, I am searching for two things, a new GPS app with similar features, I have no problem paying for a program that will do what I need, but Navigation was one of the best out there for quite a while, it was hard to find a smooth scrolling GPS app.
Anyway, my point is that the two programs are NOT the same, actually, they're not really even similar in a lot of ways aside from being map and routing programs, and for the people who used it, there's a great amount of functionality suddenly lost no matter how much you play with the new application. (And yes, I'm looking at the people who, in all caps no less, have said the two are the same application and seem to be suggesting that people just can't figure out how to use it.)