I experienced in a relatively small environment that the Discovery Wizard in SCOM 2012 is running forever.
I rejected some pending agents which were discovered properly but stayed in a “Installation in progress” state. After I rejected these agents and wanted to re-discover these servers the Discovery Wizard kept runnig forever.
Marnix Wolf has written a blog post about issues in SCOM 2007.
In my case first I stopped the “System Center Management” service on my management server after that I renamed the “Health Service State” folder to “Health Service State_old” and started the “System Center Management” service.
Now the Discovery Wizard worked like a charm.
It seems that this problem still persists in SCOM 2012.