I looked at properties on a 10.1 file geodatabase that I created that was performing slowly. Noticed that the one feature class in there has an index FDO_OBJECTID_1 that it must have inherited from the source county parcel file geodatabase, and that the "Add" button to add an attribute index is greyed out. What's going on there? Is this a clue by it takes this geodatabase to handle its 29 features?
What I did was select several batches of parcels from a county parcel 10.1 file geodatabase feature class, made several shapefiles, edited some lines, then APPENDed the several batches of polygons into a feature class of a new file geodatabase. Then I did a join with a table from the original geodatabase just to calculate a new field with Field Calculator, then dropped the join. I only have 29 records in this new feature class, so I couldn't figure out why, after dropping the join, calculating values for two other new fields was taking so long. When I thought about adding an index to improve performance I saw that there already was one, FDO_OBJECT_ID_1, and no other index is permitted. There is a spatial index called FDO_SHAPE.
Looking back at the source geodatabase, the parcel feature class has an attribute index OBJECTID and the add index button is greyed out, and no spatial index. It also has three relationship classes that I did not use in the new simplified geodatabase.
However, the copy of the whole parcel layer I made back into the old geodatabase has an attribute index FDO_OBJECTID, the "Add" button is available, and a spatial index FDO_SHAPE was created. The relationship classes were also preserved in the new copy.