This isn't a high priority, because it isn't something we desperately need .. but it would be rather convenient and kinda cool, so I'm putting it in:
It would be useful to be able to configure the verification system independently for different load or save profiles , i.e. for the profile to include specifying which verification checks run for that particular load or save.
For example, I run a custom check on GO to make sure each term is in one of the three "branch" namespaces (biological_process, cellular_component, or molecular_function). This check is important for GO, but obviously totally irrelevant to any other ontology I might want to load, so it would be nice to be able to turn the check on for loading GO, but leave it off for other ontologies.