Shapefiles are larger, slower, and less flexible than file geodatabases. Most importantly, they
are "lossy" (what you get out isn't what you put in -- truncating column names, restricting
string fields to 254 characters, no international character support, poor resolution on dates,
"zeroification" of NULL numeric values,...). I can't think of one reason to use shapefiles when
a file geodatabase is an option.
- V