Ability to create custom column mapping. For example, if I've already created the structure of list in destination, I'd like to map source columns to destination with the ability to change data type.
Main problem encountered - migration of external data. It's not supported at all. SPMT creates columns that are used for external data in source, but it doesn't migrate the content, doesn't make them usable. So instead, custom column mapping could fix this issue - if SPMT doesn't overwrite my custom columns.