We moved from VSS6 to VSS2005 just over a year ago. The database structure is identical. The only caveat we found was if some people still used VSS6 on a database where others were using VSS2005. VSS2005 treats Unicode text files as text files, whereas VSS6 does not. Which means that when VSS2005 adds a Unicode text file, VSS6 sees it as binary (this affects csproj files among others).
Other than that, VSS2005 supports proper HTTP access to the database (provided server extensions are installed), improved LAN performance (again, with server extensions), and better file system dialogs (the nasty old ones are gone). However, the new file add dialog shows ALL files, not just the ones that aren't included.
Also, VSS2005 allows the provision of custom editors and differencing tools by file extension, which is very useful. For example, some of our XML files are encrypted, so we run a decryption tool before the difference tool by using this system, which has increased the efficiency of our review processes substantially.
There are also other tweaks here and there, mostly good but occasionally annoying.
Finally, nothing has been destroyed. In fact, there appears to have been less additional corruption in the database since the transition - but I wouldn't put this down to the new VSS as it wasn't a comprehensive test.