I like the convenience of using Manage Content and Structure to move batches of files from one document library to another, while maintaining their metadata (custom fields as well as metadata like "modified by" are brought over from the source library to the target library).
However, I have been seeing some strange and concerning results, mostly having to do with content types. In a recent example, I had a library of documents with a yes/no checkbox to allow for displaying certain of the documents in a view on the home page. Another library needed to be merged in with this one, which had the same yes/no checkbox (same column name). I recommended that my client move the files from one library to another using Manage Content and Structure. After she did this, she reported that the documents from the merged library were not apperaing on the home page view even though she had checked "Yes."
When I looked more closely at the document library, I saw that there were now two identical fields for the yes/no choice in the same document library. SharePoint had copied one over and kept the original - and the values were different in each field. (In the field properties, I saw that the system had appended "0" to one of the column names on the back-end.)
In this case, it was a simple matter of making sure all the data matched from one column to another, and then deleting the duplicate column. But in some cases (e.g., when the Move function added the "Publishing Start Date" and "Publishing End Date" fields to a document library) I've had to switch on "Allow management of content types" and hide the extra fields that were added during the move process so that my end-users wouldn't be confused by the newly-added fields.
Consider this a word of warning - Manage Content and Structure may beat Explorer View in terms of convenience and speed when moving batches of files, but it can cause unintended outcomes that could take you more time to troubleshoot and fix in the long run.