No, I don't think you're understanding this here. The problem with the default map application being the Apple maps one is that the main way most people get into the maps application is not through the springboard. It's by following a link from another app, most of the time autocreated by the OS.
Clicking those links will not launch the Google Maps app. They'll launch the Apple one. Then you'll have to copy and paste potentially two locations (if using directions) out of that map into the Google Map app in order to get where you're going. If you're in another third party app that calls the systemwide maps API (such as Twitter) you'll have to go into the application's map screen, then refer that address into the default Apple map app, THEN copy and paste the address from the Apple map app to the Google one.
The user experience of this will be absolutely horrible.
If the OS allowed you to change which map application was selected by the OS in the event of finding a location link, then you could change it to the Google Maps app, and all would be fine. But you can't, and you can't do it in any other area so it ain't likely Apple are going to give you a choice.
Even worse for everyone all round, the OS now takes online links to the web based Google Maps (which are prevalent online) and directs them to the native app. Under iOS6 since the native app will be Apple's there's no chance of this continuing (it would be illegal without Google's permission, and WTF would Google allow it?). It's impossible to create a web link that launches a third party application in iOS, so these links couldn't point towards a new iOS Google maps app.
So now most of the links on the internet, which used to send us to a great native app, will instead end up linking to a ****** Google webapp, and webapps always suck. And you'll have to go through the copy and paste rigmarole in reverse if you want your compass to work.
Super.