essentially, the merges were bad in that there were no merges.  I.e. developers were mostly uninformed about the need for merges and were in the habit of making identical (or almost identical) cut and paste changes to the same files across multiple branches / streams.

This has been going on for many years here.  One developer with more experience than I have with RTC is trying to do "bulk" merges to clean up the merge history, but that is still very risky and I still suspect that we may have to fallback to just creating a new baseline like I described above.

In Perforce it just made subsequent attempts to do a merge "messy" and more risky, but in RTC it will block any subsequent attempts to deliver merges because of the other changes that have been submitted on the streams without merging. 

In our case we are merging between several streams and not just changes made in multiple workspaces on the same stream.

Thanks for your help.

If "bad merges" just means "created the same change manually in both files", then I don't see that there is a problem (i.e. there is nothing you need to clean up).  The RTC merge tool just ignores identical changes in both files, so the only content that will need to be merged is the content that actually differs.  In the extreme case, where the two files are actually the same because the exact same changes have been applied to both versions, then you can just say "auto-resolve" and RTC will mark those two versions as having been merged.

Unfortunately, the changes are not always identical and some changes were not necessarily carried over to all streams/branches. 

We have now implemented this basic strategy and are now trying to move forward and get everybody used to doing merges properly.

Thanks for your help :-)