I think I know the answer to this after doing a search, but just wanted to double check in case I'm missing something. I've got some FLVs from an interactive training DVD that a client wants to use within a longer piece. AE doesn't like them, so I'm using Adobe Media Encoder to convert them to quicktimes. They basically look like crap. Output, by the way, is widescreen DV. I'm using the Animation codec and best settings... I'm guessing because the FLVs were so compressed to begin with that unless I have the original video files there's not too much I can do to make them look any better?
Compressing any media file (to FLV or anything other than a lossles codec) involves discarding some of the data (with video files, the image). So, converting/recompressing that data to another format cannot regain the discarded data/image. At best, you can use controls in editing or compression software to slightly improve specific issues like gamma/brightness, but the only way to get better quality is from the original files (or less compressed files).