Don't transcode content which doesn't require transcoding.
I often download content from RSS feeds which cotains different file types e.g. mkv and mp4. Make Vuze intelligent so that only mkv content is transcoded and mp4 content is left alone. Finally, don't bother transcoding content from SD to HD.
James Porter commented
This could also be enhanced so that softlinks to other directory and/or drives could be present in the Transcoded directory so that files that are already stored elsewhere in other directories or even drive letters would not have to be duplicated when they didnt have to be.