Develop geodatabase annotation that will display annotation that matches feature class display.
When a definition query is set, all annotation is displayed regardless of the queried features. In other words, the mapper is limited to show all annotation when he/she only want to lable specific features within a queried feature class.
The workaround for this is to create a definition query on the feature class and then join the feature class via the objectid to the annotation layer via featureID. Once joined a query can be performed on the annotation to match the feature class query. Note, geodatabase annotation cannot be created from Maplex label engine labels.
It would be very beneficial, cartographically speaking, to have the annotation relate to the feature class and reflect queries so that the map does not have labels appearing where there are no features. It would also be helpful to create geodatabase annotation with labels created in Maplex Label Engine. Currently there are issue with the two.