For a few months, I had both the WC created QuickTime movie and an mp6 files running on my Weather Cam page. I could see no difference in the quality, even when using full-screen. The main difference was the speed they loaded! The mp4 was usually finished with the movie by the time the .mov file started! And that was on Safari, which should be able to handle .mov files better than any other PC. Obviously the files are smaller and that helps in up and downloading, I was surprised at how much faster the displaying was, however.
I've switched to uploading only mp4 files. This decreases the uploading efforts of WC. I still get FTP Overload ererz about once a week, however. I was advised to follow the "If it ain't broken any worse than that, just ignore it" technique. I'm also applying that technique to some other minor problems and it has decreased my my blood pressure and frustration levels nicely.
I use a (paid) converter app that simply watches the folder that WC normally uses and automatically converts it to mp4. I'm fairly sure Handbrake can be enabled to do this with "folder actions" enabled. Just never had time to learn the rather technical details and setup of HB.
I then have a simple Automator app that renames it and uploads it. Lastly, I have a couple of LaunchAgents that up that clean up the directories, deleting any files in it so it is ready for another file in the next hour. That also helps when Comcast breaks its connect to the interweb; twice this week!
I use another LaunchAgent to Quit and Restart the converter app once a week, just in case there is a memory leak! Otherwise, that app is running 24/7.
I don't trust Apple to maintain QuickTime much longer. I'm not sure how long plugins for it will be available, either.