There is no preferences available from the EMF Compare UI in 2.1 yet. These are planned for inclusion, but we've focused on the core for now.
As for "resource set" comparison, this is the default for EMF Compare 2. That popup was only there to avoid breaking existing users of EMF Compare 1 by allowing them to fall back to single resource... but that is too bug-prone to be recommanded (since merges could thus break the model integrity). If you were using "complete resource set", then the default behavior of 2.1 will be sufficient for you.
Jörn Guy Süß Messages: 83 Registered: July 2009 Location: Germany
I have seen in the new and noteworthy of 2.1 that the feature (disable ID use) can be set programmatically. Any hints on how I could write myself a hack to make this the default. I am thinking about sticking a patch feature on the comparison tool to change the default while we wait for the UI update.