Google already does this. Android is free for anyone to use, but if you want the Market and the Google branded Apps, you have to go through a round of certification. The process is testing for compatibility, among other things.
(This is the reason we keep seeing cheap Android tablets pop up without the Market application installed - they haven't gone through the process.)
Most carrier/OEM customization of Android is at the UI level. As a developer, it's understandable to not have all the different devices with different capabilities, but if you code as recommended and don't make assumptions about what the user has / doesn't have available, your application will work pretty much anywhere that the Market is installed.
Null Pointer Exceptions don't happen because the phone's OEM or carrier changed something - they happen because the code went ahead and assumed something worked correctly that did not.
(NPEs are the most common reason I've personally seen applications crash on my own devices, I have no data to support an assertion that that is the main cause of Force Closes, however)
As for Java, it is my impression that most JVM languages can be used on Android, though dynamic languages suffer a bit on startup time. Scala seems like a good option here.