Can you share you're gotchas using Content and Structure? I've tried it and it seems to be ok (works with Pages / Versioning, etc), but would just like to be aware if there are any.
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I did not see any drawbacks as in this method all your versioning and metadata field preserve. Only thing i found you cannot move the folder or list itself. You have to create blank list and then move the items. http://blog.henryong.com/2008/01/21/how-to-movemigrate-sharepoint-list-itemsdocuments-and-preserve-metadata-properties-at-the-same-time/
Another thing, when you move the subsite then URL will be new and if you hardcoded it you need to update.